From d4fb636818d861b097cab8250c2c7c119f5696de Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Tue, 9 May 2023 13:24:26 -0700
Subject: [PATCH 01/22] Updating the check for existing environments so that
 the full name must match

---
 setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.sh b/setup.sh
index 8834649c..f211feac 100755
--- a/setup.sh
+++ b/setup.sh
@@ -138,7 +138,7 @@ else
 fi
 
 # Check if the conda environment $env_name exists
-if conda env list | grep -q "$env_name"; then
+if conda env list | grep -q "^${env_name}\s"; then
   echo
   echo "The Conda environment $env_name already exists."
   echo "    1) Update environment"

From 645ae04b7ecc4ac281baa4d6e22d448d03bbbf7e Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Tue, 9 May 2023 13:25:35 -0700
Subject: [PATCH 02/22] Updating dependency lockfiles and adding
 environment.yml for Python 3.10

---
 conda/conda-linux-64.lock  | 580 ++++++++++++++++++++-----------------
 conda/conda-osx-64.lock    | 519 +++++++++++++++++----------------
 conda/environment_3.10.yml |  24 ++
 3 files changed, 611 insertions(+), 512 deletions(-)
 create mode 100644 conda/environment_3.10.yml

diff --git a/conda/conda-linux-64.lock b/conda/conda-linux-64.lock
index 88ba3f65..9375b26c 100644
--- a/conda/conda-linux-64.lock
+++ b/conda/conda-linux-64.lock
@@ -1,319 +1,369 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: ef26dba2670179c6605442a613aa0567cc43b352efe64eaefbb5399ddc41e110
+# input_hash: 386423d3fd437ed5ab8d93992e37ac376d3150e9382b9052856bb6dd00423a1e
 @EXPLICIT
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-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2#41e4e87062433e283696cf384f952ef6
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda#f5c65075fc34438d5b456c7f3f5ab695
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+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
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diff --git a/conda/environment_3.10.yml b/conda/environment_3.10.yml
new file mode 100644
index 00000000..7fce6c3c
--- /dev/null
+++ b/conda/environment_3.10.yml
@@ -0,0 +1,24 @@
+name: tinyrna
+channels:
+  - bioconda
+  - main
+dependencies:
+  - python>=3.10
+  - bioconductor-deseq2==1.38.0
+  - bowtie==1.3.1
+  - cython==0.29.34
+  - fastp==0.23.2
+  - htseq==2.0.2
+  - nodejs==18.12.1
+  - numpy==1.24.3
+  - pandas==2.0.1
+  - pip==23.1.2
+  - setuptools==67.7.2
+  - conda-forge::cwltool==3.1.20230425144158
+  - conda-forge::matplotlib==3.7.1
+  - conda-forge::mscorefonts==0.0.1
+  - conda-forge::psutil==5.9.5
+  - conda-forge::r-base==4.2.2
+  # tinyRNA codebase must be installed via pip in root project dir
+variables:
+  - PYTHONNOUSERSITE: 1
\ No newline at end of file

From 4663d5b2927fe82a08b73abb4eddd2114be10ac6 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Tue, 9 May 2023 13:26:03 -0700
Subject: [PATCH 03/22] Updating links to matplotlib documentation

---
 doc/Configuration.md                               | 2 +-
 doc/tiny-plot.md                                   | 2 +-
 tests/testdata/config_files/tinyrna-light.mplstyle | 2 +-
 tiny/templates/tinyrna-light.mplstyle              | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/Configuration.md b/doc/Configuration.md
index 7d9c663e..ef520f90 100644
--- a/doc/Configuration.md
+++ b/doc/Configuration.md
@@ -176,4 +176,4 @@ Examples:
 All selectors are case-insensitive.
 
 ## Plot Style Sheet Details
-Matplotlib uses key-value "rc parameters" to allow for customization of its properties and styles, and one way these parameters can be specified is with a [matplotlibrc file](https://matplotlib.org/3.5.2/tutorials/introductory/customizing.html#a-sample-matplotlibrc-file), which we simply refer to as the Plot Style Sheet. You can obtain a copy of the default style sheet used by tiny-plot with the command `tiny get-templates`, and your modified style sheet can be passed using the [plot_style_sheet parameter](Parameters.md#style-sheet). Please keep in mind that tiny-plot overrides these defaults for a few specific elements of certain plots. Feel free to reach out if there is a plot style you wish to override but find you are unable to.
\ No newline at end of file
+Matplotlib uses key-value "rc parameters" to allow for customization of its properties and styles, and one way these parameters can be specified is with a [matplotlibrc file](https://matplotlib.org/3.7.1/tutorials/introductory/customizing.html#a-sample-matplotlibrc-file), which we simply refer to as the Plot Style Sheet. You can obtain a copy of the default style sheet used by tiny-plot with the command `tiny get-templates`, and your modified style sheet can be passed using the [plot_style_sheet parameter](Parameters.md#style-sheet). Please keep in mind that tiny-plot overrides these defaults for a few specific elements of certain plots. Feel free to reach out if there is a plot style you wish to override but find you are unable to.
\ No newline at end of file
diff --git a/doc/tiny-plot.md b/doc/tiny-plot.md
index d594cb08..7879c04b 100644
--- a/doc/tiny-plot.md
+++ b/doc/tiny-plot.md
@@ -130,6 +130,6 @@ You can filter which classes are displayed using [plot_class_scatter_filter](Par
 If all features have 0 reads for a given class in one of the compared conditions, then that class is omitted from the plot and legend due to the plot's log scale. Zero-count classes will be supported in a future release.
 
 #### Customizing Group Colors
-If you find that two groups of interest share proximity and are too similar in color, you can change the group's color with a modified Plot Style Sheet. Group colors are assigned from the `axes.prop_cycle` color cycler when there are fewer groups than colors, or from the [tab20](https://matplotlib.org/3.5.2/tutorials/colors/colormaps.html#qualitative) colormap when groups outnumber colors. First, the total list of unique classes is gathered from the counts table and sorted, and the resulting list of classes is assigned colors in the order produced by the cycler. 
+If you find that two groups of interest share proximity and are too similar in color, you can change the group's color with a modified Plot Style Sheet. Group colors are assigned from the `axes.prop_cycle` color cycler when there are fewer groups than colors, or from the [tab20](https://matplotlib.org/3.7.1/tutorials/colors/colormaps.html#qualitative) colormap when groups outnumber colors. First, the total list of unique classes is gathered from the counts table and sorted, and the resulting list of classes is assigned colors in the order produced by the cycler. 
 
 For example, changing the color of the miRNA group in the above plot means changing the 6th color in the `axes.prop_cycle` list (assuming all classes are represented in the plot). The P value outgroup is always the same color and doesn't affect the assignment process. See the [config file documentation](Configuration.md#plot-style-sheet-details) for more info about the Plot Style Sheet.
\ No newline at end of file
diff --git a/tests/testdata/config_files/tinyrna-light.mplstyle b/tests/testdata/config_files/tinyrna-light.mplstyle
index 79642acd..f1e74447 100644
--- a/tests/testdata/config_files/tinyrna-light.mplstyle
+++ b/tests/testdata/config_files/tinyrna-light.mplstyle
@@ -1,6 +1,6 @@
 # Matplotlib style sheet for Small RNA plots
 # === DOCUMENTATION for this version ===============================================================
-# https://matplotlib.org/3.5.2/tutorials/introductory/customizing.html#the-default-matplotlibrc-file
+# https://matplotlib.org/3.7.1/tutorials/introductory/customizing.html#the-default-matplotlibrc-file
 
 #### Figure basics ####
 savefig.dpi: 300
diff --git a/tiny/templates/tinyrna-light.mplstyle b/tiny/templates/tinyrna-light.mplstyle
index 79642acd..f1e74447 100644
--- a/tiny/templates/tinyrna-light.mplstyle
+++ b/tiny/templates/tinyrna-light.mplstyle
@@ -1,6 +1,6 @@
 # Matplotlib style sheet for Small RNA plots
 # === DOCUMENTATION for this version ===============================================================
-# https://matplotlib.org/3.5.2/tutorials/introductory/customizing.html#the-default-matplotlibrc-file
+# https://matplotlib.org/3.7.1/tutorials/introductory/customizing.html#the-default-matplotlibrc-file
 
 #### Figure basics ####
 savefig.dpi: 300

From 7ed138d61ab5cc90719c07dc4964de6c86d30543 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Tue, 9 May 2023 13:27:33 -0700
Subject: [PATCH 04/22] Updating deprecated Pandas API calls

---
 tiny/rna/counter/statistics.py | 4 ++--
 tiny/rna/plotterlib.py         | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tiny/rna/counter/statistics.py b/tiny/rna/counter/statistics.py
index a3afd0fd..a1ec3902 100644
--- a/tiny/rna/counter/statistics.py
+++ b/tiny/rna/counter/statistics.py
@@ -219,7 +219,7 @@ def print_warnings(self):
 
 class FeatureCounts(MergedStat):
     def __init__(self, Features_obj):
-        self.feat_counts_df = pd.DataFrame(index=set.union(*Features_obj.classes.values()))
+        self.feat_counts_df = pd.DataFrame(index=pd.MultiIndex.from_tuples(set.union(*Features_obj.classes.values())))
         self.feat_counts_df.index.names = ["Feature ID", "Classifier"]
         self.aliases = Features_obj.aliases
         self.finalized = False
@@ -388,7 +388,7 @@ def _finalize_assigned(self, assigned: DefaultDict[str, Counter]) -> pd.DataFram
 
         # Drop non-nucleotide columns if they don't contain counts
         assigned_nt_len_df.drop([
-            col for col, values in assigned_nt_len_df.iteritems()
+            col for col, values in assigned_nt_len_df.items()
             if col not in ['A', 'T', 'G', 'C'] and values.isna().all()
         ], axis='columns', inplace=True)
 
diff --git a/tiny/rna/plotterlib.py b/tiny/rna/plotterlib.py
index 08fba8ec..59ec1e70 100644
--- a/tiny/rna/plotterlib.py
+++ b/tiny/rna/plotterlib.py
@@ -134,7 +134,7 @@ def barh_proportion(self, prop_ds: pd.Series, max_prop=1.0, scale=2, **kwargs) -
         text_colors = plt.get_cmap("Greys")
 
         # Create the plot and set plot attributes
-        cbar = (prop_ds * 100).plot(kind='barh', ax=ax, color=bar_colors, sort_columns=False, **kwargs)
+        cbar = (prop_ds * 100).plot(kind='barh', ax=ax, color=bar_colors, **kwargs)
         cbar.set_xlabel('Percentage of reads')
         cbar.set_xlim(0, min([(max_prop * 100) + 10, 100]))
 

From 8bdf51355bedf8ee9030e2494b764eed5cac1969 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Tue, 9 May 2023 13:27:51 -0700
Subject: [PATCH 05/22] Updating deprecated Numpy API call

---
 tiny/rna/plotterlib.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiny/rna/plotterlib.py b/tiny/rna/plotterlib.py
index 59ec1e70..8a780758 100644
--- a/tiny/rna/plotterlib.py
+++ b/tiny/rna/plotterlib.py
@@ -389,7 +389,7 @@ def get_scatter_view_lims(counts_df: pd.DataFrame, vmin: int = None, vmax: int =
         x1 = counts_df.max().max()
         minpos = 1e-300
 
-        if not np.isfinite([x0, x1]).all() or not isinstance(x0, np.float) or x1 <= 0:
+        if not np.isfinite([x0, x1]).all() or not isinstance(x0, float) or x1 <= 0:
             print("The provided dataset contains invalid values.", file=sys.stderr)
             return (minpos, minpos)
 

From 193e8b2a2582df1542307974eee6c7706c43a099 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Tue, 9 May 2023 13:28:12 -0700
Subject: [PATCH 06/22] Updating deprecated Matplotlib API call

---
 tiny/rna/plotterlib.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tiny/rna/plotterlib.py b/tiny/rna/plotterlib.py
index 8a780758..6bef4819 100644
--- a/tiny/rna/plotterlib.py
+++ b/tiny/rna/plotterlib.py
@@ -723,5 +723,7 @@ def __init__(self):
         self.ax.set_aspect('equal')
 
     def get(self) -> Tuple[plt.Figure, plt.Axes]:
-        if len(self.ax.collections): self.ax.collections.clear()
+        for group in self.ax.collections:
+            group.remove()
+
         return self.fig, self.ax
\ No newline at end of file

From df861029b69af516388f3cf39b799299e909e672 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Thu, 18 May 2023 16:00:07 -0700
Subject: [PATCH 07/22] Adding Pysam 0.21 dependency to environment_3.10.yml.
 For some reason the prior solve only pushed it to 0.20 which is incompatible
 with Apple's M1/M2 processors. Updating lock files accordingly.

---
 conda/conda-linux-64.lock  | 35 +++++++---------
 conda/conda-osx-64.lock    | 81 ++++++++++++++++++--------------------
 conda/environment_3.10.yml |  1 +
 3 files changed, 55 insertions(+), 62 deletions(-)

diff --git a/conda/conda-linux-64.lock b/conda/conda-linux-64.lock
index 9375b26c..777c1b20 100644
--- a/conda/conda-linux-64.lock
+++ b/conda/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 386423d3fd437ed5ab8d93992e37ac376d3150e9382b9052856bb6dd00423a1e
+# input_hash: 39c48ec0a4e6e75d46b0800a3ee43aa523dca20394c190a83e6ebb989bd3e1bc
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
@@ -17,7 +17,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-12.2.0-h3b97bd3_19.tar.bz2#277d373b57791ee71cafc3c5bfcf0641
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60
 https://conda.anaconda.org/conda-forge/linux-64/mscorefonts-0.0.1-2.tar.bz2#c9fd57fc9f2c51ff7b049b64fba8a7df
-https://conda.anaconda.org/conda-forge/noarch/poppler-data-0.4.12-hd8ed1ab_0.conda#d8d7293c5b37f39b2ac32940621c6592
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda#4eb33d14d794b0f4be116443ffed3853
 https://conda.anaconda.org/main/noarch/tzdata-2023c-h04d1e81_0.tar.bz2#a815d3bdb160bcc71687f2dda70d3ca4
 https://conda.anaconda.org/main/noarch/fonts-anaconda-1-h8fa9717_0.tar.bz2#7a445a2d9fbe2a88de8f09e9527f4ce1
@@ -35,7 +34,6 @@ https://conda.anaconda.org/main/linux-64/c-ares-1.19.0-h5eee18b_0.tar.bz2#d1db3a
 https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hc118613_107.conda#28b2b46b350ddb6a01d061392f75af54
 https://conda.anaconda.org/main/linux-64/fribidi-1.0.10-h7b6447c_0.tar.bz2#65d93572c4ff2ee0cc8241221aee7f12
 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37
-https://conda.anaconda.org/main/linux-64/giflib-5.2.1-h5eee18b_3.tar.bz2#6485f51176cf651b3b28c3548cef10ad
 https://conda.anaconda.org/main/linux-64/gmp-6.2.1-h295c915_3.tar.bz2#4f4570f23a92244101431ec46a235436
 https://conda.anaconda.org/main/linux-64/graphite2-1.3.14-h295c915_1.tar.bz2#09fcddfe703ce76b4b2d7dd0b6d2f928
 https://conda.anaconda.org/main/linux-64/gsl-2.7.1-h6e86dc7_1.tar.bz2#2b007d0d86d2bc680c640e51aa4ae2ce
@@ -62,7 +60,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f
 https://conda.anaconda.org/conda-forge/linux-64/libudev1-253-h0b41bf4_0.conda#6c2addbd9aa4ee47c76d50c9f0df8cd6
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/main/linux-64/libuv-1.44.2-h5eee18b_0.tar.bz2#38d0241e44b98801852916b56825115a
-https://conda.anaconda.org/main/linux-64/libwebp-base-1.2.4-h5eee18b_1.tar.bz2#ce401f477b09d371d89e008143e2a223
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.0-h0b41bf4_0.conda#0d4a7508d8c6c65314f2b9c1f56ad408
 https://conda.anaconda.org/main/linux-64/libxcb-1.13-h1bed415_1.tar.bz2#a30332027922e249a80c25faea2f3b34
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41
 https://conda.anaconda.org/main/linux-64/lz4-c-1.9.4-h6a678d5_0.tar.bz2#f24adbfdfe16b0bac0d14640bb5ce616
@@ -84,7 +82,7 @@ https://conda.anaconda.org/main/linux-64/xz-5.2.10-h5eee18b_1.tar.bz2#4adc6af158
 https://conda.anaconda.org/main/linux-64/yaml-0.2.5-h7b6447c_0.tar.bz2#fcff4f33bb4e3fa91f8d5c3168807abb
 https://conda.anaconda.org/conda-forge/linux-64/blas-1.1-openblas.tar.bz2#c259e7a3ea775c6dcba191072cab3adb
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9b5aca60558d02ddaa09d599e55920
-https://conda.anaconda.org/bioconda/linux-64/fastp-0.23.2-h5f740d0_3.tar.bz2#001589355bded3e913b0c7740d39ac10
+https://conda.anaconda.org/bioconda/linux-64/fastp-0.23.2-h5f740d0_4.tar.bz2#c71858bc9c68354909cc6fa3e47169eb
 https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-12.2.0-hcc96c02_19.tar.bz2#bb48ea333c8e6dcc159a1575f04d869e
 https://conda.anaconda.org/conda-forge/linux-64/jack-1.9.22-h11f4161_0.conda#504fa9e712b99494a9cf4630e3ca7d78
 https://conda.anaconda.org/main/linux-64/jq-1.6-h27cfd23_1000.tar.bz2#e275805740c3196af07e2b9375f303a1
@@ -97,7 +95,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.b
 https://conda.anaconda.org/conda-forge/linux-64/libflac-1.4.2-h27087fc_0.tar.bz2#7daf72d8e2a8e848e11d63ed6d1026e0
 https://conda.anaconda.org/conda-forge/linux-64/libgpg-error-1.46-h620e276_0.conda#27e745f6f2e4b757e95dd7225fbe6bdb
 https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hdcd2b5c_0.conda#c42b460bae0365fb9777b1ff9d09a554
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_1.conda#32565f92ca100184c67509d1d91c858a
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.41.2-h2797004_1.conda#1d002bf709048f8021c32abfd0e0d395
 https://conda.anaconda.org/main/linux-64/libssh2-1.10.0-h8f2d780_0.tar.bz2#f99f13daacf379a329e041ec148c4db7
 https://conda.anaconda.org/main/linux-64/libvorbis-1.3.7-h7b6447c_0.tar.bz2#e2260ef2263c0747bb17dc3622620928
 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.3-hca2bb57_4.conda#bb808b654bdc3c783deaf107a2ffb503
@@ -134,7 +132,6 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h7f98852_
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.2.1-h7f98852_2.tar.bz2#60d6eec5273f1c9af096c10c268912e3
 https://conda.anaconda.org/main/linux-64/zstd-1.5.5-hc292b87_0.tar.bz2#4e99328768f538f33aecebdae9472744
 https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-hd4edc92_1.tar.bz2#6c72ec3e660a51736913ef6ea68c454b
-https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.81.0-he95ae9e_0.conda#bbd81de5abcf7434074f37cb5fe0eaa3
 https://conda.anaconda.org/main/linux-64/brotli-1.0.9-h5eee18b_7.tar.bz2#712827b1699cc71e6240626c413408f3
 https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.9.14-ha770c72_1.tar.bz2#5746d6202ba2abad4a4707f2a2462795
 https://conda.anaconda.org/main/linux-64/freetype-2.12.1-h4a9f257_0.tar.bz2#a5dc8677d891dff2393b63189a3ad42f
@@ -153,7 +150,7 @@ https://conda.anaconda.org/main/linux-64/tktable-2.10-h14c3975_0.tar.bz2#6814c3b
 https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.0.8-pyhd8ed1ab_0.conda#0b3460f5bf4ae27dfd72fdcccc9667a9
 https://conda.anaconda.org/conda-forge/noarch/bagit-1.8.1-pyhd8ed1ab_0.tar.bz2#fb50f22b353ed3a12f5e8b7c01b58832
 https://conda.anaconda.org/main/linux-64/boltons-23.0.0-py310h06a4308_0.tar.bz2#99a4d1e0a1a8e987d3be965299b53749
-https://conda.anaconda.org/bioconda/linux-64/bowtie-1.3.1-py310h4070885_4.tar.bz2#0e93eb23d5dfce04dedc94038cb6aef1
+https://conda.anaconda.org/bioconda/linux-64/bowtie-1.3.1-py310h4070885_5.tar.bz2#11d08cea8bb9d2d9077858e6054cdcdb
 https://conda.anaconda.org/conda-forge/noarch/certifi-2023.5.7-pyhd8ed1ab_0.conda#5d1b71c942b8421285934dad1d891ebc
 https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.1.0-pyhd8ed1ab_0.conda#7fcff9f6f123696e940bda77bd4d6551
 https://conda.anaconda.org/conda-forge/linux-64/cheetah3-3.2.6.post2-py310h5764c6d_3.tar.bz2#48475e7787fe4ba62bcee1e56a48b90b
@@ -161,7 +158,7 @@ https://conda.anaconda.org/conda-forge/linux-64/click-8.1.3-py310hff52083_1.tar.
 https://conda.anaconda.org/conda-forge/linux-64/curl-7.87.0-h6312ad2_0.conda#e6ca70adeae12dce14cbf412b58ace64
 https://conda.anaconda.org/main/noarch/cycler-0.11.0-pyhd3eb1b0_0.tar.bz2#dfb0ca8055c9a72aaca7b845a6edea17
 https://conda.anaconda.org/conda-forge/linux-64/cython-0.29.34-py310heca2aa9_0.conda#95df2fa9ba55f438014e8381927f8da0
-https://conda.anaconda.org/conda-forge/linux-64/docutils-0.19-py310hff52083_1.tar.bz2#21b8fa2179290505e607f5ccd65b01b0
+https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20-py310hff52083_0.conda#880b62ca6bfcb627d6bebd1ea49cd6fe
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
 https://conda.anaconda.org/main/linux-64/future-0.18.3-py310h06a4308_0.tar.bz2#1ecaaf4df042c71443d80e235b51a5f6
 https://conda.anaconda.org/conda-forge/linux-64/glib-2.76.2-hfc55251_0.conda#00c19ae01a69fb4e1a3fb3e83094dedf
@@ -171,7 +168,6 @@ https://conda.anaconda.org/main/noarch/jsonpointer-2.1-pyhd3eb1b0_0.tar.bz2#f412
 https://conda.anaconda.org/main/linux-64/kiwisolver-1.4.4-py310h6a678d5_0.tar.bz2#1728f1fe8a6b260a1097d5723defc547
 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.14-h6ed2654_0.tar.bz2#dcc588839de1445d90995a0a2c4f3a39
 https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_h3e3d535_1.conda#a3a0f7a6f0885f5e1e0ec691566afb77
-https://conda.anaconda.org/main/linux-64/libwebp-1.2.4-h11a3e52_1.tar.bz2#4d9ed911c0455fa67680ee67d1c12a50
 https://conda.anaconda.org/main/linux-64/lockfile-0.12.2-py310h06a4308_0.tar.bz2#0792ec30a4583e05098504850e36c4e3
 https://conda.anaconda.org/main/linux-64/lxml-4.9.2-py310h5eee18b_0.tar.bz2#a883d16d137c9444c9b8ecf5ba6c6663
 https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.2-py310h1fa729e_0.conda#a1f0db6709778b77b5903541eeac4032
@@ -206,7 +202,7 @@ https://conda.anaconda.org/main/noarch/toml-0.10.2-pyhd3eb1b0_0.tar.bz2#c879bdd2
 https://conda.anaconda.org/main/linux-64/tomli-2.0.1-py310h06a4308_0.tar.bz2#c484ebee52415c809546b14d9d87b391
 https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.11.8-pyha770c72_0.conda#75838e8556166263a82038b51d01d5f1
 https://conda.anaconda.org/main/linux-64/toolz-0.12.0-py310h06a4308_0.tar.bz2#38dac546077abb0c9721f655c381c7e6
-https://conda.anaconda.org/conda-forge/linux-64/tornado-6.3-py310h1fa729e_0.conda#7c08afb0f02d5673de8e4f6f535663a8
+https://conda.anaconda.org/conda-forge/linux-64/tornado-6.3.2-py310h2372a71_0.conda#1c510e74c87dc9b8fe1f7f9e8dbcef96
 https://conda.anaconda.org/main/linux-64/tqdm-4.65.0-py310h2f386ee_0.tar.bz2#8db7239ae56fe0026c80a98aea04691b
 https://conda.anaconda.org/main/linux-64/typing_extensions-4.5.0-py310h06a4308_0.tar.bz2#9e2b2fb7dbd24c37e117637728ac69b2
 https://conda.anaconda.org/main/linux-64/unicodedata2-15.0.0-py310h5eee18b_0.tar.bz2#c7d7f380d88b9ea20f2a428f4c37f272
@@ -221,7 +217,7 @@ https://conda.anaconda.org/conda-forge/linux-64/cairo-1.16.0-ha61ee94_1014.tar.b
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-https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.39.3-py310h1fa729e_0.conda#4f39f656d6ff2761d698e69af952be82
+https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.39.4-py310h2372a71_0.conda#76426eaff204520e719207700359a855
 https://conda.anaconda.org/main/linux-64/gdk-pixbuf-2.42.10-h5eee18b_0.tar.bz2#91d63f5353a1cb1c1a2bead12511acc8
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@@ -232,7 +228,7 @@ https://conda.anaconda.org/main/noarch/jsonpatch-1.32-pyhd3eb1b0_0.tar.bz2#933be
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+https://conda.anaconda.org/conda-forge/linux-64/pillow-9.2.0-py310h454ad03_3.tar.bz2#eb354ff791f505b1d6f13f776359d88e
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@@ -247,8 +243,7 @@ https://conda.anaconda.org/conda-forge/noarch/cwlformat-2022.02.18-pyhd8ed1ab_0.
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+https://conda.anaconda.org/conda-forge/noarch/platformdirs-3.5.1-pyhd8ed1ab_0.conda#e2be672aece1f060adf7154f76531a35
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@@ -269,8 +264,8 @@ https://conda.anaconda.org/conda-forge/linux-64/r-base-4.2.2-h6b4767f_2.conda#8f
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-https://conda.anaconda.org/main/linux-64/graphviz-2.50.0-h1b29801_1.tar.bz2#bd9ed3ea11c0408b55b132e504b3530e
+https://conda.anaconda.org/bioconda/linux-64/bioconductor-zlibbioc-1.44.0-r42hc0cfd56_1.tar.bz2#9ed76d61249346184959ca3daeed7d6d
+https://conda.anaconda.org/main/linux-64/graphviz-2.50.0-h3cd0ef9_0.tar.bz2#ebb2f2f69725fd1dcfb9f8de2f82b5bd
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@@ -343,7 +338,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-openssl-2.0.5-r42hb1dc35e_0.co
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+https://conda.anaconda.org/conda-forge/linux-64/schema-salad-8.4.20230511084951-py310h2372a71_0.conda#46ec97c430adf49cccea9bb42d77d996
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@@ -351,11 +346,11 @@ https://conda.anaconda.org/bioconda/linux-64/bioconductor-xvector-0.38.0-r42hc0c
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+https://conda.anaconda.org/conda-forge/noarch/r-httr-1.4.6-r42hc72bb7e_0.conda#2f878e15055c4a19f12ac4db97cf551c
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-https://conda.anaconda.org/conda-forge/noarch/cwl-utils-0.25-pyhc268e32_0.conda#47fea91a246ae52f0137017d0886c494
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diff --git a/conda/conda-osx-64.lock b/conda/conda-osx-64.lock
index 79c13832..c61b0f77 100644
--- a/conda/conda-osx-64.lock
+++ b/conda/conda-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 577f5c6c1176b776e514aaef44e7ab48f671a93b5967987669cdd3cad85cb699
+# input_hash: 35a0becc7186ff02d2f378bf94182bec78006a44080c6055c5c520e29d28fd9d
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
 https://conda.anaconda.org/main/osx-64/bzip2-1.0.8-h1de35cc_0.tar.bz2#ab3b4e83407001e7f1603ca1fa0f4873
@@ -22,7 +22,6 @@ https://conda.anaconda.org/main/osx-64/libev-4.33-h9ed2024_1.tar.bz2#849fdd014c2
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@@ -34,39 +33,34 @@ https://conda.anaconda.org/conda-forge/noarch/mscorefonts-0.0.1-3.tar.bz2#1e88c0
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@@ -75,19 +69,18 @@ https://conda.anaconda.org/main/osx-64/libssh2-1.10.0-h0a4fc7d_0.tar.bz2#4041fb6
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 https://conda.anaconda.org/main/osx-64/requests-2.29.0-py310hecd8cb5_0.tar.bz2#b22b00aa831d9d4bb245b52b5aa35d13
 https://conda.anaconda.org/main/osx-64/cachecontrol-0.12.11-py310hecd8cb5_1.tar.bz2#047b75656cd7010710c6c0e1cc90e927
 https://conda.anaconda.org/conda-forge/osx-64/clang_osx-64-16.0.1-hac0a0c4_1.conda#fe62ac2612b93dab371096301103d128
 https://conda.anaconda.org/main/osx-64/conda-23.3.1-py310hecd8cb5_0.tar.bz2#93279e05f97fc63ccc960f636b5e0b7e
 https://conda.anaconda.org/conda-forge/noarch/galaxy-util-22.1.1-pyhd8ed1ab_0.tar.bz2#8a6d099ca1bb78a14141d132947a2f70
-https://conda.anaconda.org/main/osx-64/pydot-1.4.2-py310hecd8cb5_0.tar.bz2#22c0bc1d47f460d42b3d516c72fa5fa3
+https://conda.anaconda.org/main/osx-64/numpy-1.24.3-py310he50c29a_0.tar.bz2#29f4f4f78a84e8946b3aa6369e9df5f3
+https://conda.anaconda.org/conda-forge/osx-64/pydot-1.4.2-py310h2ec42d9_3.tar.bz2#70b74c0b2233a61842bae7e309c4a503
 https://conda.anaconda.org/main/noarch/pydotplus-2.0.2-py_3.tar.bz2#cfb123d1e6b3375ae2acab4c290390ae
 https://conda.anaconda.org/conda-forge/osx-64/clangxx_osx-64-16.0.1-h950475c_1.conda#e794792c5758b6b1694786c17ec49b92
+https://conda.anaconda.org/conda-forge/osx-64/contourpy-1.0.7-py310ha23aa8a_0.conda#bc714cc57ec6422105ed991167987a9d
 https://conda.anaconda.org/conda-forge/noarch/galaxy-containers-22.1.1-pyhd8ed1ab_0.tar.bz2#f31587a27d77a1d9e3e0f02abf231ef0
 https://conda.anaconda.org/main/osx-64/gfortran_osx-64-11.3.0-h96634ac_0.tar.bz2#15b706365cad9247f6a04ccd72b77a41
+https://conda.anaconda.org/conda-forge/osx-64/pandas-2.0.1-py310h5e4fcda_1.conda#24acbaa1a659e357cba1ad1cf4eb9bac
 https://conda.anaconda.org/conda-forge/noarch/prov-1.5.1-py_1.tar.bz2#66e578dc9f4bfe65728ad547a81cd6dd
-https://conda.anaconda.org/conda-forge/osx-64/schema-salad-8.4.20230426093816-py310h6729b98_0.conda#6db0a247ba47da4b762c3db997440a20
+https://conda.anaconda.org/conda-forge/osx-64/schema-salad-8.4.20230511084951-py310h6729b98_0.conda#2a897cb9914db6d63c1e353207c69561
 https://conda.anaconda.org/conda-forge/noarch/cwl-upgrader-1.2.6-pyhd8ed1ab_0.conda#8bf402bd12b3c4ff81a526e2eb442c65
 https://conda.anaconda.org/conda-forge/noarch/galaxy-tool-util-22.1.5-pyhd8ed1ab_0.tar.bz2#01e03f88ef58292e3faa017714bb015f
-https://conda.anaconda.org/conda-forge/osx-64/r-base-4.2.2-h6e3643f_2.conda#52be862a98170c470a17903eedd070dc
+https://conda.anaconda.org/main/osx-64/matplotlib-base-3.7.1-py310ha533b9c_1.tar.bz2#7ffa357f191641321c69f6a357074f4a
+https://conda.anaconda.org/conda-forge/osx-64/r-base-4.2.2-h490d416_1.tar.bz2#d9f56140ffdfd0ebe21326efccfefe39
 https://conda.anaconda.org/bioconda/noarch/bioconductor-biocgenerics-0.44.0-r42hdfd78af_0.tar.bz2#ad7705e81b15e89b8aac79e3c7e0c596
 https://conda.anaconda.org/bioconda/noarch/bioconductor-data-packages-20230420-hdfd78af_0.tar.bz2#1ff71c9ad48852a18f5e7847a81bdb15
-https://conda.anaconda.org/bioconda/osx-64/bioconductor-zlibbioc-1.44.0-r42h3be46a4_0.tar.bz2#f0247fc359022387768d20ef598e515f
-https://conda.anaconda.org/conda-forge/noarch/cwl-utils-0.25-pyhc268e32_0.conda#47fea91a246ae52f0137017d0886c494
+https://conda.anaconda.org/bioconda/osx-64/bioconductor-zlibbioc-1.44.0-r42h3be46a4_1.tar.bz2#6469fb018e9ed5b5e8a0013969b81494
+https://conda.anaconda.org/conda-forge/noarch/cwl-utils-0.26-pyhc268e32_1.conda#914b183e38c91680f768a199643b67b5
+https://conda.anaconda.org/bioconda/osx-64/htseq-2.0.2-py310hec0d4ff_0.tar.bz2#ce4a5b08e033cef5540f749b93d1c950
+https://conda.anaconda.org/conda-forge/osx-64/matplotlib-3.7.1-py310h2ec42d9_0.conda#958029c1236746d27149fca648c41cab
 https://conda.anaconda.org/conda-forge/noarch/r-bh-1.81.0_1-r42hc72bb7e_0.conda#4e21ae5b780964cbe738d42af30b5dd5
 https://conda.anaconda.org/conda-forge/osx-64/r-bit-4.0.5-r42h815d134_0.tar.bz2#da9570dcb48c8fd3f1021a914254c7a9
 https://conda.anaconda.org/conda-forge/osx-64/r-bitops-1.0_7-r42h815d134_1.tar.bz2#ad14e33a18b6dbcbb0bc51618ef18303
@@ -270,7 +267,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.1-r42hc72bb7e_1.
 https://conda.anaconda.org/conda-forge/noarch/r-withr-2.5.0-r42hc72bb7e_1.tar.bz2#aa5c3e131a8e5a1c9576f484afa86c51
 https://conda.anaconda.org/conda-forge/osx-64/r-xml-3.99_0.14-r42h67ce8dc_0.conda#1bcfec9f43fd535f728832dc6099f746
 https://conda.anaconda.org/conda-forge/noarch/r-xtable-1.8_4-r42hc72bb7e_4.tar.bz2#28a6bce0b87124a67a28d99568432c78
-https://conda.anaconda.org/bioconda/osx-64/bioconductor-biobase-2.58.0-r42h3be46a4_0.tar.bz2#2824b9348014583081fda9959019e08e
+https://conda.anaconda.org/bioconda/osx-64/bioconductor-biobase-2.58.0-r42h4c50009_1.tar.bz2#0ec3acd3ced3927aacaaa51f3798329c
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0.tar.bz2#4af93b040f3a44af5804ab44066ee7cd
 https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.10.0-r42hdfd78af_0.tar.bz2#5ef80e5c26d03a75d62e2ee02054e665
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-s4vectors-0.36.0-r42h3be46a4_0.tar.bz2#14feffa61b725d7dbe43e24dd9164087
@@ -286,7 +283,7 @@ https://conda.anaconda.org/conda-forge/osx-64/r-matrix-1.5_4-r42hce01bf1_0.conda
 https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.0-r42hc72bb7e_1005.tar.bz2#e7c53fd2064700ff07429966a7da7508
 https://conda.anaconda.org/conda-forge/osx-64/r-nlme-3.1_162-r42h1e4e481_0.conda#9655986da096423520f48b1ffa7f3325
 https://conda.anaconda.org/conda-forge/osx-64/r-rcpparmadillo-0.12.2.0.0-r42hf5e6a41_0.conda#71494d027f0aa82d470b812288638049
-https://conda.anaconda.org/conda-forge/osx-64/r-rcurl-1.98_1.10-r42h815d134_0.conda#dce748afe7f60db226acfcb7bc2845f4
+https://conda.anaconda.org/conda-forge/osx-64/r-rcurl-1.98_1.12-r42h815d134_0.conda#c5a483726862d0f3b1a789475221accd
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-iranges-2.32.0-r42h3be46a4_0.tar.bz2#071093e9be31af88c3ddce1e30589e56
 https://conda.anaconda.org/conda-forge/noarch/r-futile.logger-1.4.3-r42hc72bb7e_1004.tar.bz2#7b9365f78e1f2fe8d36a1e3c74ec6856
 https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.3-r42hc72bb7e_0.conda#3d7ba7ed44328d61a94837f19780f3c0
@@ -301,7 +298,7 @@ https://conda.anaconda.org/bioconda/osx-64/bioconductor-delayedarray-0.24.0-r42h
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodb-1.34.9-r42hdfd78af_0.tar.bz2#10961a4cf078c3e368caa1465a45feca
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-xvector-0.38.0-r42h3be46a4_0.tar.bz2#c43771da3c506a73df699e8a166b0d17
 https://conda.anaconda.org/conda-forge/noarch/r-blob-1.2.4-r42hc72bb7e_0.conda#c1ca3fcfc8cbff48ccd3796e22c9daf9
-https://conda.anaconda.org/conda-forge/noarch/r-httr-1.4.5-r42hc72bb7e_0.conda#4ef716635774c8aa6ff0cf3f35eba7e3
+https://conda.anaconda.org/conda-forge/noarch/r-httr-1.4.6-r42hc72bb7e_0.conda#2f878e15055c4a19f12ac4db97cf551c
 https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r42hc72bb7e_0.conda#3ee1760065c70c190878381582ef1d41
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-biostrings-2.66.0-r42h3be46a4_0.tar.bz2#b2d641dcfb6d364221478c3f8741a044
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-genomicranges-1.50.0-r42h3be46a4_0.tar.bz2#3c73655c683c98faeffa80d1a1a0e707
diff --git a/conda/environment_3.10.yml b/conda/environment_3.10.yml
index 7fce6c3c..1bbd2816 100644
--- a/conda/environment_3.10.yml
+++ b/conda/environment_3.10.yml
@@ -13,6 +13,7 @@ dependencies:
   - numpy==1.24.3
   - pandas==2.0.1
   - pip==23.1.2
+  - pysam==0.21.0
   - setuptools==67.7.2
   - conda-forge::cwltool==3.1.20230425144158
   - conda-forge::matplotlib==3.7.1

From 383dd1d2a4067539aae8792540a5a66890aeb207 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Thu, 18 May 2023 16:02:41 -0700
Subject: [PATCH 08/22] Changing the default StepVector from HTSeq to Cython in
 the ReferenceBase class. This makes it consistent with the current argparse
 config

---
 tiny/rna/counter/hts_parsing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index ec27df54..2574c895 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -393,7 +393,7 @@ class ReferenceBase(ABC):
     """The base class for reference parsers"""
 
     def __init__(self, **prefs):
-        self.stepvector = prefs.get('stepvector', 'HTSeq')
+        self.stepvector = prefs.get('stepvector', 'Cython')
         self.feats = self._init_genomic_array()
 
         # The selector is assigned whenever get() is called.

From 8a4cd3dc7a077924129087636a30bbefe58ea52e Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Thu, 18 May 2023 16:03:40 -0700
Subject: [PATCH 09/22] Updating update-lockfiles.sh to allow for passing the
 environment file name as a commandline parameter. The default filename
 remains environment.yml

---
 conda/update-lockfiles.sh | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/conda/update-lockfiles.sh b/conda/update-lockfiles.sh
index f2fab3ab..5ee7ab4e 100755
--- a/conda/update-lockfiles.sh
+++ b/conda/update-lockfiles.sh
@@ -1,5 +1,12 @@
 #!/usr/bin/env bash
 
+# USAGE: if you would like to specify a different environment file,
+# you can pass the preferred filename as the first argument to the script.
+# Otherwise, environment.yml is used.
+#   ./update-lockfiles.sh preferred_file
+
+[[ $# -eq 1 ]] && env_file=$1 || env_file="environment.yml"
+
 dev_env_name="tinyrna_dev_v1.0"
 dev_deps="conda-forge::conda-lock python=3.9"
 
@@ -66,14 +73,14 @@ conda activate "${dev_env_name}"
 
 # Update Linux lockfile
 status "Updating linux-64 lockfile..."
-conda-lock lock --kind explicit --platform linux-64 --file environment.yml > "linux_lockfile.log" 2>&1
+conda-lock lock --kind explicit --platform linux-64 --file "$env_file" > "linux_lockfile.log" 2>&1
 
 # Check result for Linux lockfile
 check_lockfile_update_status $?
 
 # Update macOS lockfile
 status "Updating osx-64 lockfile..."
-conda-lock lock --kind explicit --platform osx-64 --file environment.yml > "osx_lockfile.log" 2>&1
+conda-lock lock --kind explicit --platform osx-64 --file "$env_file" > "osx_lockfile.log" 2>&1
 
 # Check result for OSX lockfile
 check_lockfile_update_status $?
\ No newline at end of file

From 4f407fc896723ca83ea59b70fc6a037519301b22 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Fri, 19 May 2023 13:04:19 -0700
Subject: [PATCH 10/22] Cleaning up script argument handling by using parameter
 expansion

---
 conda/update-lockfiles.sh | 10 +++++-----
 setup.sh                  |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/conda/update-lockfiles.sh b/conda/update-lockfiles.sh
index 5ee7ab4e..9bb39792 100755
--- a/conda/update-lockfiles.sh
+++ b/conda/update-lockfiles.sh
@@ -1,11 +1,11 @@
 #!/usr/bin/env bash
 
-# USAGE: if you would like to specify a different environment file,
-# you can pass the preferred filename as the first argument to the script.
-# Otherwise, environment.yml is used.
-#   ./update-lockfiles.sh preferred_file
+# USAGE: provide the filename for the desired environment version.
+# Lock files will be produced for linux-64 and osx-64.
+#   ./update-lockfiles.sh ENVIRONMENT_FILE.yml
 
-[[ $# -eq 1 ]] && env_file=$1 || env_file="environment.yml"
+usage="Usage: $(basename "$0") ENVIRONMENT_FILE.yml"
+env_file=${1:? $usage}
 
 dev_env_name="tinyrna_dev_v1.0"
 dev_deps="conda-forge::conda-lock python=3.9"
diff --git a/setup.sh b/setup.sh
index f211feac..8d2a5215 100755
--- a/setup.sh
+++ b/setup.sh
@@ -4,7 +4,7 @@
 # you can pass the preferred name as the first argument to the script:
 #   ./setup.sh preferred_name
 
-[[ $# -eq 1 ]] && env_name=$1 || env_name="tinyrna"
+env_name=${1:-tinyrna}
 
 python_version="3.9"
 miniconda_version="4.12.0"

From de7623b1f4fecc8a73a5a03141dd63eb24db28d7 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 21 May 2023 17:58:05 -0700
Subject: [PATCH 11/22] Adding a template environment.yml file. This file will
 be used for creating environments for yet-unsupported versions of Python

---
 conda/environment_template.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 conda/environment_template.yml

diff --git a/conda/environment_template.yml b/conda/environment_template.yml
new file mode 100644
index 00000000..19cdf459
--- /dev/null
+++ b/conda/environment_template.yml
@@ -0,0 +1,25 @@
+name: tinyrna
+channels:
+  - bioconda
+  - main
+dependencies:
+  - python>={PYTHON_VERSION}
+  - pysam>=0.21.0  # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in
+  - bioconductor-deseq2
+  - bowtie
+  - cython
+  - fastp
+  - htseq
+  - nodejs
+  - numpy
+  - pandas
+  - pip
+  - setuptools
+  - conda-forge::cwltool
+  - conda-forge::matplotlib
+  - conda-forge::mscorefonts
+  - conda-forge::psutil
+  - conda-forge::r-base
+  # tinyRNA codebase must be installed via pip in root project dir
+variables:
+  - PYTHONNOUSERSITE: 1
\ No newline at end of file

From c5ef7b82257ece9d4b3d31b322e53e55f21c9ccd Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 21 May 2023 17:58:32 -0700
Subject: [PATCH 12/22] Including some recent updates in environment_3.10.yml.
 Also making pinning format consistent

---
 conda/environment_3.10.yml | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/conda/environment_3.10.yml b/conda/environment_3.10.yml
index 1bbd2816..47dd8d57 100644
--- a/conda/environment_3.10.yml
+++ b/conda/environment_3.10.yml
@@ -4,22 +4,22 @@ channels:
   - main
 dependencies:
   - python>=3.10
-  - bioconductor-deseq2==1.38.0
-  - bowtie==1.3.1
-  - cython==0.29.34
-  - fastp==0.23.2
-  - htseq==2.0.2
-  - nodejs==18.12.1
-  - numpy==1.24.3
-  - pandas==2.0.1
-  - pip==23.1.2
-  - pysam==0.21.0
-  - setuptools==67.7.2
-  - conda-forge::cwltool==3.1.20230425144158
-  - conda-forge::matplotlib==3.7.1
-  - conda-forge::mscorefonts==0.0.1
-  - conda-forge::psutil==5.9.5
-  - conda-forge::r-base==4.2.2
+  - pysam>=0.21.0  # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in
+  - bioconductor-deseq2=1.38.0
+  - bowtie=1.3.1
+  - cython=0.29.34
+  - fastp=0.23.3
+  - htseq=2.0.3
+  - nodejs=18.12.1
+  - numpy=1.24.3
+  - pandas=2.0.1
+  - pip=23.1.2
+  - setuptools=67.7.2
+  - conda-forge::cwltool=3.1.20230425144158
+  - conda-forge::matplotlib=3.7.1
+  - conda-forge::mscorefonts=0.0.1
+  - conda-forge::psutil=5.9.5
+  - conda-forge::r-base=4.2.2
   # tinyRNA codebase must be installed via pip in root project dir
 variables:
   - PYTHONNOUSERSITE: 1
\ No newline at end of file

From 8f08834ba9acc0f9e10335cad7daa6455c51e120 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 21 May 2023 17:58:54 -0700
Subject: [PATCH 13/22] Renaming environment.yml to environment_3.9.yml for
 consistency

---
 conda/{environment.yml => environment_3.9.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename conda/{environment.yml => environment_3.9.yml} (100%)

diff --git a/conda/environment.yml b/conda/environment_3.9.yml
similarity index 100%
rename from conda/environment.yml
rename to conda/environment_3.9.yml

From 6d4401e3086889ae350fdf8f4a403da2b1404562 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 21 May 2023 17:59:25 -0700
Subject: [PATCH 14/22] Updating lockfiles to include recent updates to
 environment_3.10.yml

---
 conda/conda-linux-64.lock | 40 ++++++++++-----------
 conda/conda-osx-64.lock   | 74 ++++++++++++++++++++-------------------
 2 files changed, 58 insertions(+), 56 deletions(-)

diff --git a/conda/conda-linux-64.lock b/conda/conda-linux-64.lock
index 777c1b20..fd2d4ba5 100644
--- a/conda/conda-linux-64.lock
+++ b/conda/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 39c48ec0a4e6e75d46b0800a3ee43aa523dca20394c190a83e6ebb989bd3e1bc
+# input_hash: d2e01a5f5550ed17bdc79ab7e2bf7f11f14a867d5d35a86e8fe994e4d4784963
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
@@ -82,7 +82,7 @@ https://conda.anaconda.org/main/linux-64/xz-5.2.10-h5eee18b_1.tar.bz2#4adc6af158
 https://conda.anaconda.org/main/linux-64/yaml-0.2.5-h7b6447c_0.tar.bz2#fcff4f33bb4e3fa91f8d5c3168807abb
 https://conda.anaconda.org/conda-forge/linux-64/blas-1.1-openblas.tar.bz2#c259e7a3ea775c6dcba191072cab3adb
 https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9b5aca60558d02ddaa09d599e55920
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diff --git a/conda/conda-osx-64.lock b/conda/conda-osx-64.lock
index c61b0f77..ff842a72 100644
--- a/conda/conda-osx-64.lock
+++ b/conda/conda-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 35a0becc7186ff02d2f378bf94182bec78006a44080c6055c5c520e29d28fd9d
+# input_hash: f8e5fc867c0e7ed169eb89eb612ecf959da065a05fb895c7ec6def12a1fb46ee
 @EXPLICIT
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@@ -92,12 +97,11 @@ https://conda.anaconda.org/conda-forge/noarch/bagit-1.8.1-pyhd8ed1ab_0.tar.bz2#f
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@@ -105,8 +109,8 @@ https://conda.anaconda.org/main/noarch/jsonpointer-2.1-pyhd3eb1b0_0.tar.bz2#f412
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@@ -115,13 +119,14 @@ https://conda.anaconda.org/conda-forge/noarch/mistune-2.0.5-pyhd8ed1ab_0.conda#6
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+https://conda.anaconda.org/bioconda/osx-64/bioconductor-biocparallel-1.32.5-r42hc0ef7c4_1.tar.bz2#e85ae00326200c84345f46834bb7f9ff
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-delayedarray-0.24.0-r42h3be46a4_0.tar.bz2#9bae5ab108a4fc208c4c54b478dc68c0
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodb-1.34.9-r42hdfd78af_0.tar.bz2#10961a4cf078c3e368caa1465a45feca
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-xvector-0.38.0-r42h3be46a4_0.tar.bz2#c43771da3c506a73df699e8a166b0d17

From 06b7e9bcba8d4f55b194372d05ece98cf7d79cd0 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 21 May 2023 18:03:33 -0700
Subject: [PATCH 15/22] Adding a script and accompanying documentation for
 creating new environment.yml files and for updating lockfiles from a given
 environment file.

---
 conda/README.md           |  40 +++++++
 conda/env.py              | 235 ++++++++++++++++++++++++++++++++++++++
 conda/update-lockfiles.sh |  86 --------------
 3 files changed, 275 insertions(+), 86 deletions(-)
 create mode 100644 conda/README.md
 create mode 100644 conda/env.py
 delete mode 100755 conda/update-lockfiles.sh

diff --git a/conda/README.md b/conda/README.md
new file mode 100644
index 00000000..4ad6535e
--- /dev/null
+++ b/conda/README.md
@@ -0,0 +1,40 @@
+# For Users
+These files are utilized during tinyRNA's setup. During normal usage you shouldn't need to access or modify them. To install or update the tinyRNA environment and codebase, navigate to the project's root directory and run `./setup.sh`
+
+# For Developers
+Environment lockfiles allow us to skip Conda's time-intensive preparation steps, e.g. "Solving environment" and "Collecting package metadata", when the user installs/updates the tinyRNA environment.
+
+Dependencies are strictly pinned so that the user's environment exactly matches the environment where testing has been performed.
+
+## Files in this Directory
+| File                       | Description                                                                                                                                                                                                           |
+|----------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `environment_3.[...].yml`  | Environment files for different Python versions. These files are platform-agnostic to simplify testing. Just one environment file is needed for creating both the Linux and macOS lockfiles.                          |
+| `environment_template.yml` | Template environment file used for creating new environment files for a specific Python version.                                                                                                                      |
+| `conda-[...]-64.lock`      | Platform-specific lockfiles that contain a fully solved dependency tree specification for the latest Python version we support. These are the files that the setup script uses when creating the tinyRNA environment. | 
+| `env.py`                   | A script for creating and updating these files.                                                                                                                                                                       |
+
+## The Development Environment
+A separate conda environment is created to hold the dependencies required for creating and updating lockfiles. Keeping development and tinyRNA dependencies separate helps to avoid dependency conflicts.
+
+## Updating the Default Python Version
+An environment's Python version determines the environment's dependency tree. Creating specifications for a new Python version is a multi-step process, but a script has been provided to help automate it. **The script can be executed from any environment.**
+
+The idea is to start with a template environment file containing all of our dependencies where nearly all dependencies are unpinned. Normally only the Python version is pinned in the template, but right now Pysam is also pinned because Mamba doesn't currently solve for the version we need by default. We then use Mamba to solve the unpinned dependency versions which are used to create a final, strictly pinned environment file for the new Python version. The new file is then used to create platform-specific lockfiles.
+
+### 1. Create an Environment File for the new Python Version
+```shell
+python3 env.py new-env --py 3.XX --template environment_template.yml
+```
+
+Replace `3.XX` with the target Python version. This command will produce a new environment file named `environment_3.XX.yml` that contains each dependency's solved version.
+
+### 2. Create Platform-Specific Lockfiles
+```shell
+python3 env.py update-locks --env-file environment_3.XX.yml
+```
+
+Replace `environment_3.XX.yml` with the name of the environment file you created in step 1. This command will rebuild the dependency tree in both lockfiles (linux and osx) according to the new environment file.
+
+
+
diff --git a/conda/env.py b/conda/env.py
new file mode 100644
index 00000000..fa085418
--- /dev/null
+++ b/conda/env.py
@@ -0,0 +1,235 @@
+import subprocess
+import itertools
+import argparse
+import json
+import sys
+import os
+
+from tempfile import TemporaryDirectory, NamedTemporaryFile
+from typing import Dict
+
+dev_env_name = "tinyrna_dev_v1.1"
+dev_py_vers = "3.9"
+dev_deps = [
+    "conda=22.9",  # Only for compatibility with conda-lock=1.4.0 (see https://github.com/conda/conda-lock/issues/408)
+    "python=" + dev_py_vers,
+    "conda-forge::mamba=1.4.2",
+    "conda-forge::conda-lock=1.4.0",
+]
+
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    subcommands = parser.add_subparsers(
+        title="Available subcommands",
+        description=f"Use `python3 {os.path.basename(__file__)} <subcommand> -h` for subcommand details.",
+        required=True,
+        dest="command"
+    )
+
+    new_env = subcommands.add_parser("new-env", help="Create an environment.yml file for a new Python version.")
+    new_env.add_argument(
+        "--py",
+        help='The target Python version formatted as "3.XX".',
+        required=True
+    )
+    new_env.add_argument(
+        "--template",
+        help="The environment file to serve as a template for the new file. Dependencies should be minimally pinned.",
+        required=True
+    )
+
+    update_lock = subcommands.add_parser("rebuild-locks", help="Rebuild osx-64 and linux-64 lockfiles from env-file.")
+    update_lock.add_argument(
+        "--env-file",
+        help="The environment[...].yml to use for rebuilding lockfiles.",
+        required=True
+    )
+
+    return parser.parse_args()
+
+
+def get_conda_envs() -> Dict[str, str]:
+    """Returns a dict of {env_name: env_path} for all conda environments."""
+
+    proc = subprocess.run(
+        ["conda", "env", "list"],
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        encoding="utf-8"
+    )
+
+    # Check for errors
+    try:
+        proc.check_returncode()
+        raw_env_list = proc.stdout
+    except subprocess.CalledProcessError:
+        print(proc.stderr, file=sys.stderr)
+        sys.exit("Failed to get conda environment list.")
+
+    envs = [line.replace('*', ' ').split(' ', 1)
+            for line in raw_env_list.splitlines()
+            if len(line) and line[0] not in ("#", " ")]
+
+    return {env_name.strip(): env_path.strip()
+            for env_name, env_path in envs}
+
+
+def get_dev_env_path() -> str:
+    """Returns the path to the dev environment, creating it if necessary."""
+
+    print("Checking for dev environment ...")
+
+    envs = get_conda_envs()
+    if dev_env_name in envs:
+        print("Dev environment found.")
+        return envs[dev_env_name]
+
+    with open("dev_env_create.log", 'w') as log:
+        print(f"Creating dev environment {dev_env_name} ...")
+        proc = subprocess.run(
+            ["conda", "create",
+             "--name", dev_env_name,
+             "--yes",  *dev_deps],
+            stdout=log, stderr=log,
+            encoding="utf-8"
+        )
+
+    try:
+        proc.check_returncode()
+        print("Dev environment created.")
+    except subprocess.CalledProcessError:
+        sys.exit("Failed to create dev environment. See dev_env_create.log for details.")
+
+    return get_conda_envs()[dev_env_name]
+
+
+def mamba_solve(env_file, env_prefix) -> Dict[str, str]:
+    """Calls Mamba subprocess to solve the env_file specs and returns the result as a dict
+    of {package_name: package_version}.
+
+    This function is a reduced version of conda_lock.conda_solver.solve_specs_for_arch()."""
+
+    # Call mamba from the dev environment regardless of the current environment
+    env_ctx =   ["conda", "run", "-n", dev_env_name]
+    solve_cmd = ["mamba", "env", "create",
+                 "--file", env_file.name,
+                 "--prefix", env_prefix,
+                 "--dry-run",
+                 "--json"]
+
+    print("Solving target environment ...")
+    proc = subprocess.run(
+        env_ctx + solve_cmd,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        encoding="utf-8"
+    )
+
+    # Check for errors
+    try:
+        proc.check_returncode()
+    except subprocess.CalledProcessError:
+        try:
+            err_json = json.loads(proc.stdout)
+            message = err_json.get("message", err_json)
+        except json.JSONDecodeError as e:
+            print(f"Failed to parse json, {e}", file=sys.stderr)
+            message = proc.stdout
+        sys.exit(message)
+
+    # Parse the output
+    proc_stdout = proc.stdout
+    json_resp = json.loads(proc_stdout[proc_stdout.index("{"): proc_stdout.rindex("}") + 1])
+    actions = json_resp["actions"]
+
+    # Return a dict of {package_name: package_version}
+    return {
+        pkg["name"]: pkg["version"]
+        for pkg in itertools.chain(actions['FETCH'], actions['LINK'])
+    }
+
+
+def new_env_file(env_template, py_version, dev_env_path):
+    """Creates a new environment file for the given Python version by solving the template with mamba and pinning"""
+
+    # The dev environment's /bin first needs to be prepended to PATH in main()
+    import ruamel.yaml
+
+    yaml = ruamel.yaml.YAML()
+    with open(env_template) as template, \
+            TemporaryDirectory() as tmp_prefix, \
+            NamedTemporaryFile('w+', suffix=".yml") as tmp_env_file:
+
+        # Update Python version in the template contents and write it to a temporary file
+        versioned_template = yaml.load(template.read().replace("{PYTHON_VERSION}", py_version))
+        yaml.dump(versioned_template, tmp_env_file)
+        tmp_env_file.flush()
+
+        # Get the complete environment spec by solving the template with mamba
+        solved_versions = mamba_solve(tmp_env_file, tmp_prefix)
+
+    # Pin each unpinned dependency in the template with its solved version
+    for i, spec in enumerate(versioned_template["dependencies"]):
+        if set(spec) & {"=", "<", ">"}:  # Skip pinned template specs
+            continue
+
+        spec_no_channel = spec.split("::")[-1]
+        version = solved_versions[spec_no_channel]
+        versioned_template["dependencies"][i] = f"{spec}={version}"
+
+    # Write the new environment file
+    output_file = f"environment_{py_version}.yml"
+    with open(output_file, 'w') as f:
+        yaml.dump(versioned_template, f)
+        print(f"Created environment file: {output_file}")
+
+
+def rebuild_lockfiles(env_file):
+    """Rebuilds the osx-64 and linux-64 lockfiles from the provided environment file."""
+
+    supported_platforms = ["osx-64", "linux-64"]
+    env_ctx = ["conda", "run", "-n", dev_env_name]  # Run command from dev environment regardless of current env
+
+    for platform in supported_platforms:
+        lock_cmd = ["conda-lock",
+                    "--file", env_file,
+                    "--kind", "explicit",
+                    "--platform", platform]
+
+        print(f"Building {platform} lockfile ...")
+        proc = subprocess.run(
+            env_ctx + lock_cmd,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+            encoding="utf-8"
+        )
+
+        try:
+            proc.check_returncode()
+        except subprocess.CalledProcessError:
+            log_file = f"{platform}_lockfile.log"
+            with open(log_file, 'w') as f:
+                f.write(proc.stdout)
+            sys.exit(f"Error occurred while rebuilding the {platform} lockfile. See {log_file}.")
+
+        print(f"{platform} lockfile complete.")
+
+
+def main():
+    args = get_args()
+    denv = get_dev_env_path()
+
+    # Import modules from dev env from here forward
+    sys.path.insert(0, os.path.join(denv, "lib", f"python{dev_py_vers}", "site-packages"))
+
+    if args.command == "new-env":
+        new_env_file(args.template, args.py, denv)
+    if args.command == "rebuild-locks":
+        rebuild_lockfiles(args.env_file)
+
+    print("Done.")
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/conda/update-lockfiles.sh b/conda/update-lockfiles.sh
deleted file mode 100755
index 9bb39792..00000000
--- a/conda/update-lockfiles.sh
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/usr/bin/env bash
-
-# USAGE: provide the filename for the desired environment version.
-# Lock files will be produced for linux-64 and osx-64.
-#   ./update-lockfiles.sh ENVIRONMENT_FILE.yml
-
-usage="Usage: $(basename "$0") ENVIRONMENT_FILE.yml"
-env_file=${1:? $usage}
-
-dev_env_name="tinyrna_dev_v1.0"
-dev_deps="conda-forge::conda-lock python=3.9"
-
-#==== FUNCTION DEFINITIONS ================================================================
-
-function check_lockfile_update_status() {
-  if [[ $1 -eq 4 ]]; then
-    # Supposedly reported with --check-input-hash
-    # However this appears to not apply to subdependencies
-    success "No updates for lockfile"
-  elif [[ $1 -eq 0 ]]; then
-    success "Lockfile has been updated"
-  else
-    fail "Error occurred while updating lockfile. Please see the associated log file."
-    exit 1
-  fi
-}
-
-function success() {
-  check="✓"
-  green_on="\033[1;32m"
-  green_off="\033[0m"
-  printf "${green_on}${check} %s${green_off}\n" "$*"
-}
-
-function status() {
-  blue_on="\033[1;34m"
-  blue_off="\033[0m"
-  printf "${blue_on}%s${blue_off}\n" "$*"
-}
-
-function fail() {
-  nope="⃠"
-  red_on="\033[1;31m"
-  red_off="\033[0m"
-  printf "${red_on}${nope} %s${red_off}\n" "$*"
-}
-
-#==== MAIN ROUTINE ========================================================================
-
-# Check if os is mac or linux
-if [[ "$OSTYPE" == "darwin"* ]]; then
-  success "macOS detected"
-  shell=$(basename "$(dscl . -read ~/ UserShell | cut -f 2 -d " ")")
-elif [[ "$OSTYPE" == "linux-gnu" ]]; then
-  success "Linux detected"
-  shell="$(basename "$SHELL")"
-else
-  fail "Unsupported OS"
-  exit 1
-fi
-
-# Enable the use of Conda commands in this script
-eval "$(conda shell."$shell" hook)"
-
-# Create the dev environment if needed
-if ! conda env list | grep -q ${dev_env_name}; then
-  status "Creating ${dev_env_name} environment..."
-  conda create --name "${dev_env_name}" --yes "${dev_deps}" 2>&1 | tee "dev_env_create.log"
-fi
-
-# Activate dev environment
-conda activate "${dev_env_name}"
-
-# Update Linux lockfile
-status "Updating linux-64 lockfile..."
-conda-lock lock --kind explicit --platform linux-64 --file "$env_file" > "linux_lockfile.log" 2>&1
-
-# Check result for Linux lockfile
-check_lockfile_update_status $?
-
-# Update macOS lockfile
-status "Updating osx-64 lockfile..."
-conda-lock lock --kind explicit --platform osx-64 --file "$env_file" > "osx_lockfile.log" 2>&1
-
-# Check result for OSX lockfile
-check_lockfile_update_status $?
\ No newline at end of file

From 9172cacb522c5d84cb66dbcb4ca8eb14676d0560 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 14:01:40 -0700
Subject: [PATCH 16/22] Code cleanup and refactoring.

The rebuild-locks command now runs a vulnerability scan on the packages reported in the new lockfiles.

A make-archive command has been added to allow for making offline archives of an existing environment. The archives are os-specific. It's a simple wrapper for conda-pack.
---
 conda/env.py | 181 ++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 137 insertions(+), 44 deletions(-)

diff --git a/conda/env.py b/conda/env.py
index fa085418..4b7e5294 100644
--- a/conda/env.py
+++ b/conda/env.py
@@ -1,3 +1,10 @@
+"""This script helps manage conda environment specifications for the project.
+
+A separate development environment is created to hold its dependencies
+(Python modules and command-line utilities). The script can be executed in any environment
+and will utilize the dependencies in the dev environment via `conda run` and modification
+of the system PATH variable."""
+import platform
 import subprocess
 import itertools
 import argparse
@@ -5,16 +12,24 @@
 import sys
 import os
 
+## ADDITIONAL IMPORTS from dev environment after calling redirect_imports() ##
+
 from tempfile import TemporaryDirectory, NamedTemporaryFile
 from typing import Dict
 
+
+osx_lockfile = "conda-osx-64.lock"
+linux_lockfile = "conda-linux-64.lock"
+
 dev_env_name = "tinyrna_dev_v1.1"
 dev_py_vers = "3.9"
 dev_deps = [
     "conda=22.9",  # Only for compatibility with conda-lock=1.4.0 (see https://github.com/conda/conda-lock/issues/408)
     "python=" + dev_py_vers,
-    "conda-forge::mamba=1.4.2",
-    "conda-forge::conda-lock=1.4.0",
+    "mamba=1.4.2",
+    "conda-lock=1.4.0",
+    "jake=3.0.0",
+    "conda-pack=0.7.0"
 ]
 
 
@@ -39,13 +54,21 @@ def get_args():
         required=True
     )
 
-    update_lock = subcommands.add_parser("rebuild-locks", help="Rebuild osx-64 and linux-64 lockfiles from env-file.")
-    update_lock.add_argument(
+    rebuild_locks = subcommands.add_parser("rebuild-locks", help="Rebuild osx-64 and linux-64 lockfiles from env-file.")
+    rebuild_locks.add_argument(
         "--env-file",
         help="The environment[...].yml to use for rebuilding lockfiles.",
         required=True
     )
 
+    make_archive = subcommands.add_parser("make-archive", help="Create an environment archive for offline installation.",
+                                          description="NOTE: archive is OS-specific. Install using conda-pack.")
+    make_archive.add_argument(
+        "--env-name",
+        help="The name of the environment to archive.",
+        required=True
+    )
+
     return parser.parse_args()
 
 
@@ -90,6 +113,7 @@ def get_dev_env_path() -> str:
         proc = subprocess.run(
             ["conda", "create",
              "--name", dev_env_name,
+             "--channel", "conda-forge",
              "--yes",  *dev_deps],
             stdout=log, stderr=log,
             encoding="utf-8"
@@ -104,6 +128,67 @@ def get_dev_env_path() -> str:
     return get_conda_envs()[dev_env_name]
 
 
+class EnvSolver:
+
+    def __init__(self, template_filename):
+        self.template_filename = template_filename
+
+        import ruamel.yaml  # redirect_inputs() must be called first
+        self.yaml = ruamel.yaml.YAML()
+
+    def solve(self, py_version: str):
+        py_bounded = self.get_bounded_py_spec(py_version)
+        template_yml = self.get_template(py_bounded)
+        solved_versions = self.solve_specs(template_yml)
+        solved_template = self.get_updated_template(template_yml, solved_versions)
+
+        # Write the new environment file
+        output_file = f"environment_{py_version}.yml"
+        with open(output_file, 'w') as f:
+            self.yaml.dump(solved_template, f)
+            print(f"Created environment file: {output_file}")
+
+    def get_template(self, py_bounded: str) -> dict:
+        """Returns a parsed template for the bounded Python version"""
+
+        with open(self.template_filename, 'r') as f:
+            versioned = f.read().replace("{PYTHON_VERSION}", py_bounded)
+            return self.yaml.load(versioned)
+
+    def solve_specs(self, template_yml: dict) -> dict:
+        """Returns the solved dependency tree as a dictionary of {package_name: package_version}"""
+
+        with NamedTemporaryFile('w+', suffix=".yml") as tmp_env_file, \
+                TemporaryDirectory() as tmp_prefix:
+
+            # Write Python-versioned template to a temporary file
+            self.yaml.dump(template_yml, tmp_env_file)
+            tmp_env_file.flush()
+
+            # Get the complete environment spec by solving the template with mamba
+            solved_versions = mamba_solve(tmp_env_file, tmp_prefix)
+
+        return solved_versions
+
+    def get_updated_template(self, template_yml: dict, solutions: dict) -> dict:
+        """Updates each unpinned dependency in the template with its solved version"""
+
+        for i, spec in enumerate(template_yml["dependencies"]):
+            if set(spec) & {"=", "<", ">"}:  # Skip pinned specs
+                continue
+
+            spec_no_channel = spec.split("::")[-1]
+            version = solutions[spec_no_channel]
+            template_yml["dependencies"][i] = f"{spec}={version}"
+
+        return template_yml
+
+    def get_bounded_py_spec(self, py_version: str) -> str:
+        """Place an upper bound on the specified version to prevent the solver from overshooting"""
+        v_split = py_version.split('.')
+        return f"{py_version}, <{v_split[0]}.{int(v_split[1]) + 1}"
+
+
 def mamba_solve(env_file, env_prefix) -> Dict[str, str]:
     """Calls Mamba subprocess to solve the env_file specs and returns the result as a dict
     of {package_name: package_version}.
@@ -149,42 +234,6 @@ def mamba_solve(env_file, env_prefix) -> Dict[str, str]:
         for pkg in itertools.chain(actions['FETCH'], actions['LINK'])
     }
 
-
-def new_env_file(env_template, py_version, dev_env_path):
-    """Creates a new environment file for the given Python version by solving the template with mamba and pinning"""
-
-    # The dev environment's /bin first needs to be prepended to PATH in main()
-    import ruamel.yaml
-
-    yaml = ruamel.yaml.YAML()
-    with open(env_template) as template, \
-            TemporaryDirectory() as tmp_prefix, \
-            NamedTemporaryFile('w+', suffix=".yml") as tmp_env_file:
-
-        # Update Python version in the template contents and write it to a temporary file
-        versioned_template = yaml.load(template.read().replace("{PYTHON_VERSION}", py_version))
-        yaml.dump(versioned_template, tmp_env_file)
-        tmp_env_file.flush()
-
-        # Get the complete environment spec by solving the template with mamba
-        solved_versions = mamba_solve(tmp_env_file, tmp_prefix)
-
-    # Pin each unpinned dependency in the template with its solved version
-    for i, spec in enumerate(versioned_template["dependencies"]):
-        if set(spec) & {"=", "<", ">"}:  # Skip pinned template specs
-            continue
-
-        spec_no_channel = spec.split("::")[-1]
-        version = solved_versions[spec_no_channel]
-        versioned_template["dependencies"][i] = f"{spec}={version}"
-
-    # Write the new environment file
-    output_file = f"environment_{py_version}.yml"
-    with open(output_file, 'w') as f:
-        yaml.dump(versioned_template, f)
-        print(f"Created environment file: {output_file}")
-
-
 def rebuild_lockfiles(env_file):
     """Rebuilds the osx-64 and linux-64 lockfiles from the provided environment file."""
 
@@ -216,17 +265,61 @@ def rebuild_lockfiles(env_file):
         print(f"{platform} lockfile complete.")
 
 
+def scan_lockfiles():
+    """Scans for vulnerable packages in both lockfiles using the Sonatype OSS Index"""
+
+    env_ctx =  ["conda", "run", "--no-capture-output", "-n", dev_env_name]  # Run command from dev environment
+    scan_cmd = ["jake", "ddt", "-t", "CONDA"]
+
+    for lock in (osx_lockfile, linux_lockfile):
+        with open(lock, 'rb') as f:
+            packages = f.read()
+
+        subprocess.run(
+            env_ctx + scan_cmd,
+            input=packages
+        )
+
+        # Indicate which file the report was for
+        print('\n'.join(["", "=" * 50, f"{lock.upper()}: SCAN COMPLETE", "=" * 50]))
+
+
+def make_env_archive(env_name):
+    """Just a wrapper for conda-pack."""
+
+    reported_os = platform.system()
+    os_name = {'Darwin': "osx"}.get(reported_os, reported_os).lower()
+    archive_name = f"{env_name}_{os_name}.tar.gz"
+
+    env_ctx = ["conda", "run", "--no-capture-output", "-n", dev_env_name]  # Run command from dev environment regardless of current env
+    command = ["conda-pack",
+               "-n", env_name,
+               "-o", archive_name]
+
+    subprocess.run(env_ctx + command)
+
+
+def redirect_imports(denv):
+    """Adds the dev environment's Python site-packages location to $PATH so that
+    dependencies for this script can be imported from it. This allows the script
+    to be executed from any environment. It also allows us to create the dev
+    environment and utilize its dependencies all in the same run."""
+
+    sys.path.insert(0, os.path.join(denv, "lib", f"python{dev_py_vers}", "site-packages"))
+
+
 def main():
     args = get_args()
     denv = get_dev_env_path()
-
-    # Import modules from dev env from here forward
-    sys.path.insert(0, os.path.join(denv, "lib", f"python{dev_py_vers}", "site-packages"))
+    redirect_imports(denv)
 
     if args.command == "new-env":
-        new_env_file(args.template, args.py, denv)
+        EnvSolver(args.template).solve(args.py)
     if args.command == "rebuild-locks":
         rebuild_lockfiles(args.env_file)
+        scan_lockfiles()
+    if args.command == "make-archive":
+        make_env_archive(args.env_name)
 
     print("Done.")
 

From ab30e6905a6008c2f22cadbe1ac5e98de27c62ec Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 14:11:51 -0700
Subject: [PATCH 17/22] Adding/updating environment files with some new
 temporary pinnings that are necessary for functioning environments.

---
 conda/environment_3.10.yml     | 42 ++++++++++++++++++----------------
 conda/environment_3.9.yml      | 41 ++++++++++++++++++---------------
 conda/environment_template.yml |  4 +++-
 3 files changed, 47 insertions(+), 40 deletions(-)

diff --git a/conda/environment_3.10.yml b/conda/environment_3.10.yml
index 47dd8d57..a8dcbc42 100644
--- a/conda/environment_3.10.yml
+++ b/conda/environment_3.10.yml
@@ -1,25 +1,27 @@
 name: tinyrna
 channels:
-  - bioconda
-  - main
+- bioconda
+- main
 dependencies:
-  - python>=3.10
-  - pysam>=0.21.0  # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in
-  - bioconductor-deseq2=1.38.0
-  - bowtie=1.3.1
-  - cython=0.29.34
-  - fastp=0.23.3
-  - htseq=2.0.3
-  - nodejs=18.12.1
-  - numpy=1.24.3
-  - pandas=2.0.1
-  - pip=23.1.2
-  - setuptools=67.7.2
-  - conda-forge::cwltool=3.1.20230425144158
-  - conda-forge::matplotlib=3.7.1
-  - conda-forge::mscorefonts=0.0.1
-  - conda-forge::psutil=5.9.5
-  - conda-forge::r-base=4.2.2
+- python>=3.10, <3.11
+- pysam>=0.21.0    # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in the future
+- bioconductor-deseq2=1.38.0
+- bowtie=1.3.1
+- cython=0.29.34
+- fastp=0.23.3
+- htseq=2.0.3
+- nodejs=18.12.1
+- numpy=1.24.3
+- pandas=2.0.1
+- pip=23.1.2
+- setuptools=67.7.2
+- conda-forge::cwltool=3.1.20230425144158
+  # Mamba solves for a bad build of cwl-utils which didn't state its requirement for urllib3 <2 (likely temporary)
+- conda-forge::urllib3 <2
+- conda-forge::matplotlib=3.7.1
+- conda-forge::mscorefonts=0.0.1
+- conda-forge::psutil=5.9.5
+- conda-forge::r-base=4.2.2
   # tinyRNA codebase must be installed via pip in root project dir
 variables:
-  - PYTHONNOUSERSITE: 1
\ No newline at end of file
+- PYTHONNOUSERSITE: 1
diff --git a/conda/environment_3.9.yml b/conda/environment_3.9.yml
index 99f0d099..343489ca 100644
--- a/conda/environment_3.9.yml
+++ b/conda/environment_3.9.yml
@@ -1,24 +1,27 @@
 name: tinyrna
 channels:
-  - bioconda
-  - main
+- bioconda
+- main
 dependencies:
-  - python>=3.9
-  - bioconductor-deseq2==1.34.0
-  - bowtie==1.3.1
-  - cython==0.29.24
-  - fastp==0.23.2
-  - htseq==2.0.2
-  - nodejs==16.13.1
-  - numpy==1.23.1
-  - pandas==1.4.3
-  - pip==22.1.2
-  - setuptools==63.1.0
-  - conda-forge::cwltool==3.1.20220628170238
-  - conda-forge::matplotlib==3.5.2
-  - conda-forge::mscorefonts==0.0.1
-  - conda-forge::psutil==5.9.1
-  - conda-forge::r-base==4.1.1
+- python>=3.9, <3.10
+- pysam>=0.21.0    # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in the future
+- bioconductor-deseq2=1.38.0
+- bowtie=1.3.1
+- cython=0.29.34
+- fastp=0.23.3
+- htseq=2.0.3
+- nodejs=18.12.1
+- numpy=1.24.3
+- pandas=2.0.1
+- pip=23.1.2
+- setuptools=67.7.2
+- conda-forge::cwltool=3.1.20230425144158
+  # Mamba solves for a bad build of cwl-utils which didn't state its requirement for urllib3 <2 (likely temporary)
+- conda-forge::urllib3 <2
+- conda-forge::matplotlib=3.7.1
+- conda-forge::mscorefonts=0.0.1
+- conda-forge::psutil=5.9.5
+- conda-forge::r-base=4.2.2
   # tinyRNA codebase must be installed via pip in root project dir
 variables:
-  - PYTHONNOUSERSITE: 1
\ No newline at end of file
+- PYTHONNOUSERSITE: 1
diff --git a/conda/environment_template.yml b/conda/environment_template.yml
index 19cdf459..37cccdac 100644
--- a/conda/environment_template.yml
+++ b/conda/environment_template.yml
@@ -4,7 +4,7 @@ channels:
   - main
 dependencies:
   - python>={PYTHON_VERSION}
-  - pysam>=0.21.0  # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in
+  - pysam>=0.21.0  # 0.20 is incompatible with Apple Silicon. This is likely safe to remove in the future
   - bioconductor-deseq2
   - bowtie
   - cython
@@ -16,6 +16,8 @@ dependencies:
   - pip
   - setuptools
   - conda-forge::cwltool
+  # Mamba solves for a bad build of cwl-utils which didn't state its requirement for urllib3 <2 (likely temporary)
+  - conda-forge::urllib3 <2
   - conda-forge::matplotlib
   - conda-forge::mscorefonts
   - conda-forge::psutil

From d5da96c3009bb581e03f3f7eb75c7e172ef22c5b Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 15:03:00 -0700
Subject: [PATCH 18/22] Updating lockfiles from updated environment*.yml files.
 Also correcting syntax for exact vs. fuzzy matching for conda-forge packages
 since it appears conda-lock doesn't properly parse these specifications when
 the channel scope is also provided

---
 conda/conda-linux-64.lock  | 33 +++++++++++++++++++--------------
 conda/conda-osx-64.lock    | 22 +++++++++++-----------
 conda/environment_3.10.yml | 10 +++++-----
 conda/environment_3.9.yml  | 10 +++++-----
 4 files changed, 40 insertions(+), 35 deletions(-)

diff --git a/conda/conda-linux-64.lock b/conda/conda-linux-64.lock
index fd2d4ba5..01ac44f6 100644
--- a/conda/conda-linux-64.lock
+++ b/conda/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: d2e01a5f5550ed17bdc79ab7e2bf7f11f14a867d5d35a86e8fe994e4d4784963
+# input_hash: a902d517f1be7fb2ddc3c432b38eff63124f918ea870d561fd62818231d95e60
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
@@ -17,6 +17,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-12.2.0-h3b97bd3_19.tar.bz2#277d373b57791ee71cafc3c5bfcf0641
 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60
 https://conda.anaconda.org/conda-forge/linux-64/mscorefonts-0.0.1-2.tar.bz2#c9fd57fc9f2c51ff7b049b64fba8a7df
+https://conda.anaconda.org/conda-forge/noarch/poppler-data-0.4.12-hd8ed1ab_0.conda#d8d7293c5b37f39b2ac32940621c6592
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda#4eb33d14d794b0f4be116443ffed3853
 https://conda.anaconda.org/main/noarch/tzdata-2023c-h04d1e81_0.tar.bz2#a815d3bdb160bcc71687f2dda70d3ca4
 https://conda.anaconda.org/main/noarch/fonts-anaconda-1-h8fa9717_0.tar.bz2#7a445a2d9fbe2a88de8f09e9527f4ce1
@@ -30,10 +31,11 @@ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar
 https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2#be733e69048951df1e4b4b7bb8c7666f
 https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2#d9c69a24ad678ffce24c6543a0176b00
 https://conda.anaconda.org/main/linux-64/bzip2-1.0.8-h7b6447c_0.tar.bz2#f52e60deb7f4c82821be9a868e889348
-https://conda.anaconda.org/main/linux-64/c-ares-1.19.0-h5eee18b_0.tar.bz2#d1db3ae66648d0586b55d9c70f204a43
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda#e8c18d865be43e2fb3f7a145b6adf1f5
 https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hc118613_107.conda#28b2b46b350ddb6a01d061392f75af54
 https://conda.anaconda.org/main/linux-64/fribidi-1.0.10-h7b6447c_0.tar.bz2#65d93572c4ff2ee0cc8241221aee7f12
 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37
+https://conda.anaconda.org/main/linux-64/giflib-5.2.1-h5eee18b_3.tar.bz2#6485f51176cf651b3b28c3548cef10ad
 https://conda.anaconda.org/main/linux-64/gmp-6.2.1-h295c915_3.tar.bz2#4f4570f23a92244101431ec46a235436
 https://conda.anaconda.org/main/linux-64/graphite2-1.3.14-h295c915_1.tar.bz2#09fcddfe703ce76b4b2d7dd0b6d2f928
 https://conda.anaconda.org/main/linux-64/gsl-2.7.1-h6e86dc7_1.tar.bz2#2b007d0d86d2bc680c640e51aa4ae2ce
@@ -60,7 +62,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f
 https://conda.anaconda.org/conda-forge/linux-64/libudev1-253-h0b41bf4_0.conda#6c2addbd9aa4ee47c76d50c9f0df8cd6
 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/main/linux-64/libuv-1.44.2-h5eee18b_0.tar.bz2#38d0241e44b98801852916b56825115a
-https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.0-h0b41bf4_0.conda#0d4a7508d8c6c65314f2b9c1f56ad408
+https://conda.anaconda.org/main/linux-64/libwebp-base-1.2.4-h5eee18b_1.tar.bz2#ce401f477b09d371d89e008143e2a223
 https://conda.anaconda.org/main/linux-64/libxcb-1.13-h1bed415_1.tar.bz2#a30332027922e249a80c25faea2f3b34
 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41
 https://conda.anaconda.org/main/linux-64/lz4-c-1.9.4-h6a678d5_0.tar.bz2#f24adbfdfe16b0bac0d14640bb5ce616
@@ -116,7 +118,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-12.2.0-h5
 https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-12.2.0-hcc96c02_19.tar.bz2#698aae34e4f5e0ea8eac0d529c8f20b6
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-hf9c8cef_0.conda#5f7e9efd540d7ac4b485660231ba6150
 https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.1-h166bdaf_0.tar.bz2#f967fc95089cd247ceed56eda31de3a9
-https://conda.anaconda.org/conda-forge/linux-64/libglib-2.76.2-hebfc3b9_0.conda#db1d4a1dfc04f3eab50d97551850759a
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.76.3-hebfc3b9_0.conda#a64f11b244b2c112cd3fa1cbe9493999
 https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.9.1-hd6dc26d_0.conda#a3ede1b8e47f993ff1fe3908b23bb307
 https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_openblas.tar.bz2#955d993f41f9354bf753d29864ea20ad
 https://conda.anaconda.org/main/linux-64/libpng-1.6.39-h5eee18b_0.tar.bz2#1bffe1481ed4f88827248fb9001f8923
@@ -132,10 +134,11 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h7f98852_
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.2.1-h7f98852_2.tar.bz2#60d6eec5273f1c9af096c10c268912e3
 https://conda.anaconda.org/main/linux-64/zstd-1.5.5-hc292b87_0.tar.bz2#4e99328768f538f33aecebdae9472744
 https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-hd4edc92_1.tar.bz2#6c72ec3e660a51736913ef6ea68c454b
+https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.81.0-he95ae9e_0.conda#bbd81de5abcf7434074f37cb5fe0eaa3
 https://conda.anaconda.org/main/linux-64/brotli-1.0.9-h5eee18b_7.tar.bz2#712827b1699cc71e6240626c413408f3
 https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.9.14-ha770c72_1.tar.bz2#5746d6202ba2abad4a4707f2a2462795
 https://conda.anaconda.org/main/linux-64/freetype-2.12.1-h4a9f257_0.tar.bz2#a5dc8677d891dff2393b63189a3ad42f
-https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.76.2-hfc55251_0.conda#7147b242b00aff73d95259ff318d14a0
+https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.76.3-hfc55251_0.conda#8951eedf3cdf94dd733c1b5eee1f4880
 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h36d4200_3.conda#c9f4416a34bc91e0eb029f912c68f81f
 https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.87.0-h6312ad2_0.conda#ad07f06bd133e76e12165bc3ec2c8646
 https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.7-hadd5161_1.conda#17d91085ccf5934ce652cb448d0cb65a
@@ -161,13 +164,14 @@ https://conda.anaconda.org/conda-forge/linux-64/cython-0.29.34-py310heca2aa9_0.c
 https://conda.anaconda.org/conda-forge/linux-64/docutils-0.20.1-py310hff52083_0.conda#741a0de9f26de79576d681d950910781
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
 https://conda.anaconda.org/main/linux-64/future-0.18.3-py310h06a4308_0.tar.bz2#1ecaaf4df042c71443d80e235b51a5f6
-https://conda.anaconda.org/conda-forge/linux-64/glib-2.76.2-hfc55251_0.conda#00c19ae01a69fb4e1a3fb3e83094dedf
+https://conda.anaconda.org/conda-forge/linux-64/glib-2.76.3-hfc55251_0.conda#950e02f5665f5f4ff0437a6acba58798
 https://conda.anaconda.org/main/linux-64/humanfriendly-10.0-py310h06a4308_1.tar.bz2#0b9cbc959dd7ad9dae926ee8a97252c7
 https://conda.anaconda.org/main/linux-64/idna-3.4-py310h06a4308_0.tar.bz2#aaedbfe2ce4396b9ae3598d8b1abb21d
 https://conda.anaconda.org/main/noarch/jsonpointer-2.1-pyhd3eb1b0_0.tar.bz2#f4129d80d8832a5520403970ca2a1103
 https://conda.anaconda.org/main/linux-64/kiwisolver-1.4.4-py310h6a678d5_0.tar.bz2#1728f1fe8a6b260a1097d5723defc547
 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.14-h6ed2654_0.tar.bz2#dcc588839de1445d90995a0a2c4f3a39
 https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_h9986a30_2.conda#907344cee64101d44d806bbe0fccb01d
+https://conda.anaconda.org/main/linux-64/libwebp-1.2.4-h11a3e52_1.tar.bz2#4d9ed911c0455fa67680ee67d1c12a50
 https://conda.anaconda.org/main/linux-64/lockfile-0.12.2-py310h06a4308_0.tar.bz2#0792ec30a4583e05098504850e36c4e3
 https://conda.anaconda.org/main/linux-64/lxml-4.9.2-py310h5eee18b_0.tar.bz2#a883d16d137c9444c9b8ecf5ba6c6663
 https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.2-py310h1fa729e_0.conda#a1f0db6709778b77b5903541eeac4032
@@ -204,7 +208,7 @@ https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.11.8-pyha770c72_0.conda#
 https://conda.anaconda.org/main/linux-64/toolz-0.12.0-py310h06a4308_0.tar.bz2#38dac546077abb0c9721f655c381c7e6
 https://conda.anaconda.org/conda-forge/linux-64/tornado-6.3.2-py310h2372a71_0.conda#1c510e74c87dc9b8fe1f7f9e8dbcef96
 https://conda.anaconda.org/main/linux-64/tqdm-4.65.0-py310h2f386ee_0.tar.bz2#8db7239ae56fe0026c80a98aea04691b
-https://conda.anaconda.org/main/linux-64/typing_extensions-4.5.0-py310h06a4308_0.tar.bz2#9e2b2fb7dbd24c37e117637728ac69b2
+https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.6.1-pyha770c72_0.conda#050e6f090e0de8df4a44112cb390e21d
 https://conda.anaconda.org/main/linux-64/unicodedata2-15.0.0-py310h5eee18b_0.tar.bz2#c7d7f380d88b9ea20f2a428f4c37f272
 https://conda.anaconda.org/main/linux-64/webencodings-0.5.1-py310h06a4308_1.tar.bz2#49b82f30a2a45b2ce167a876cdc9e21c
 https://conda.anaconda.org/conda-forge/noarch/wheel-0.40.0-pyhd8ed1ab_0.conda#49bb0d9e60ce1db25e151780331bb5f3
@@ -228,13 +232,13 @@ https://conda.anaconda.org/main/noarch/jsonpatch-1.32-pyhd3eb1b0_0.tar.bz2#933be
 https://conda.anaconda.org/conda-forge/linux-64/libclang-15.0.7-default_h7634d5b_2.conda#1a4fe5162abe4a19b5a9dedf158a0ff9
 https://conda.anaconda.org/main/linux-64/libgd-2.3.3-h695aa2c_1.tar.bz2#e17d73f9dbc6791d2462d0b3ea348c65
 https://conda.anaconda.org/main/linux-64/numpy-1.24.3-py310hac523dd_0.tar.bz2#71b579009261704e229b1969cfb2fd43
-https://conda.anaconda.org/conda-forge/linux-64/pillow-9.2.0-py310h454ad03_3.tar.bz2#eb354ff791f505b1d6f13f776359d88e
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@@ -261,11 +266,11 @@ https://conda.anaconda.org/bioconda/linux-64/htseq-2.0.3-py310ha14a713_0.tar.bz2
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diff --git a/conda/conda-osx-64.lock b/conda/conda-osx-64.lock
index ff842a72..de4c5ddd 100644
--- a/conda/conda-osx-64.lock
+++ b/conda/conda-osx-64.lock
@@ -1,10 +1,10 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: f8e5fc867c0e7ed169eb89eb612ecf959da065a05fb895c7ec6def12a1fb46ee
+# input_hash: 518781a6dc99e43b8a42f37cf0a61b9b6d9a706aa9c7da406636a1db451d74b2
 @EXPLICIT
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 https://conda.anaconda.org/main/osx-64/matplotlib-base-3.7.1-py310ha533b9c_1.tar.bz2#7ffa357f191641321c69f6a357074f4a
-https://conda.anaconda.org/main/osx-64/requests-2.29.0-py310hecd8cb5_0.tar.bz2#b22b00aa831d9d4bb245b52b5aa35d13
+https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda#a30144e4156cdbb236f99ebb49828f8b
 https://conda.anaconda.org/main/osx-64/cachecontrol-0.12.11-py310hecd8cb5_1.tar.bz2#047b75656cd7010710c6c0e1cc90e927
 https://conda.anaconda.org/conda-forge/osx-64/clang_osx-64-16.0.1-hac0a0c4_1.conda#fe62ac2612b93dab371096301103d128
 https://conda.anaconda.org/main/osx-64/conda-23.3.1-py310hecd8cb5_0.tar.bz2#93279e05f97fc63ccc960f636b5e0b7e
@@ -263,7 +263,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-rcolorbrewer-1.1_3-r42h785f33e_1
 https://conda.anaconda.org/conda-forge/osx-64/r-rcpp-1.0.10-r42h49197e3_0.conda#798aa6e691c3477fd914e50b83d1c77a
 https://conda.anaconda.org/conda-forge/osx-64/r-rlang-1.1.1-r42hac7d2d5_0.conda#e5ffa7d78eff64745625b71efd9d83d2
 https://conda.anaconda.org/conda-forge/noarch/r-snow-0.4_4-r42hc72bb7e_1.tar.bz2#14bb231e001f434a37a401030ac3e7a6
-https://conda.anaconda.org/conda-forge/osx-64/r-sys-3.4.1-r42h815d134_0.tar.bz2#b1f8fe8dd22b56a053bcc241a8e2fd9d
+https://conda.anaconda.org/conda-forge/osx-64/r-sys-3.4.2-r42h6dc245f_0.conda#1ec86628065df645b0fad2c17c3cda98
 https://conda.anaconda.org/conda-forge/osx-64/r-utf8-1.2.3-r42h815d134_0.conda#7118e7a2d21ea8025e3dd1c1bc2cd54e
 https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.1-r42hc72bb7e_1.tar.bz2#412de380396e466ddb7cd48fae639072
 https://conda.anaconda.org/conda-forge/noarch/r-withr-2.5.0-r42hc72bb7e_1.tar.bz2#aa5c3e131a8e5a1c9576f484afa86c51
diff --git a/conda/environment_3.10.yml b/conda/environment_3.10.yml
index a8dcbc42..e3f22c51 100644
--- a/conda/environment_3.10.yml
+++ b/conda/environment_3.10.yml
@@ -15,13 +15,13 @@ dependencies:
 - pandas=2.0.1
 - pip=23.1.2
 - setuptools=67.7.2
-- conda-forge::cwltool=3.1.20230425144158
+- conda-forge::cwltool==3.1.20230425144158
   # Mamba solves for a bad build of cwl-utils which didn't state its requirement for urllib3 <2 (likely temporary)
 - conda-forge::urllib3 <2
-- conda-forge::matplotlib=3.7.1
-- conda-forge::mscorefonts=0.0.1
-- conda-forge::psutil=5.9.5
-- conda-forge::r-base=4.2.2
+- conda-forge::matplotlib==3.7.1
+- conda-forge::mscorefonts==0.0.1
+- conda-forge::psutil==5.9.5
+- conda-forge::r-base==4.2.2
   # tinyRNA codebase must be installed via pip in root project dir
 variables:
 - PYTHONNOUSERSITE: 1
diff --git a/conda/environment_3.9.yml b/conda/environment_3.9.yml
index 343489ca..0f7b025f 100644
--- a/conda/environment_3.9.yml
+++ b/conda/environment_3.9.yml
@@ -15,13 +15,13 @@ dependencies:
 - pandas=2.0.1
 - pip=23.1.2
 - setuptools=67.7.2
-- conda-forge::cwltool=3.1.20230425144158
+- conda-forge::cwltool==3.1.20230425144158
   # Mamba solves for a bad build of cwl-utils which didn't state its requirement for urllib3 <2 (likely temporary)
 - conda-forge::urllib3 <2
-- conda-forge::matplotlib=3.7.1
-- conda-forge::mscorefonts=0.0.1
-- conda-forge::psutil=5.9.5
-- conda-forge::r-base=4.2.2
+- conda-forge::matplotlib==3.7.1
+- conda-forge::mscorefonts==0.0.1
+- conda-forge::psutil==5.9.5
+- conda-forge::r-base==4.2.2
   # tinyRNA codebase must be installed via pip in root project dir
 variables:
 - PYTHONNOUSERSITE: 1

From 4d5a34c4f3358805d849e5508985ca78a9da6b4c Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 15:13:42 -0700
Subject: [PATCH 19/22] Lots of updates to setup.sh.

Most importantly, in-place updates to the tinyRNA environment are no longer supported. The environment must be removed and recreated. When this functionality was originally added, dependency updates were taking place within the same Python version. Now they are across Python versions, and this can cause many, many problems. I tried several approaches to preserve this functionality, and while some got close, they were not stable or reliable. This is the safest way.

Additionally:
- Updated the version of miniconda that the script installs (if necessary)
- The Apple Silicon version of Miniconda is installed, if appropriate and necessary
- The Miniconda installer is executed with bash as it appears the latest version doesn't work with zsh
- If Miniconda was installed, the user is instructed to source their shell's .rc file to finalize installation
- It is now possible to run the script from outside of the project directory
---
 README.md |  3 +++
 setup.sh  | 55 +++++++++++++++++++++++++++++++------------------------
 2 files changed, 34 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index 0287395b..9bfdf6d0 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,9 @@ This option provides the latest features but stable releases are more rigorously
  ./setup.sh
 ```
 
+### Updating an Existing Installation
+When it's time to update your installation of tinyRNA, simply repeat the procedure you used for installation. Note that the existing Conda environment, including any additional packages you may have installed within it, will be removed by the installation script.
+
 ## tiny-count Standalone Installation
 Alternatively, you can install tinyRNA's precision counting tool by itself. Unlike the full tinyRNA suite, this option can be installed in existing conda environments and requires fewer dependencies.
 
diff --git a/setup.sh b/setup.sh
index 8d2a5215..ae9069cc 100755
--- a/setup.sh
+++ b/setup.sh
@@ -5,9 +5,13 @@
 #   ./setup.sh preferred_name
 
 env_name=${1:-tinyrna}
+miniconda_version="23.3.1-0"
+cwd="$(dirname "$0")"
 
-python_version="3.9"
-miniconda_version="4.12.0"
+# This is the default Python version that will be used by Miniconda (if Miniconda requires installation).
+# Note that this isn't the same as the tinyRNA environment's Python version.
+# The tinyRNA environment's Python version is instead specified in the platform lockfile.
+miniconda_python_version="310"
 
 function success() {
   check="✓"
@@ -57,7 +61,7 @@ function verify_conda_checksum() {
 function setup_environment() {
   # Setup tinyRNA environment using our generated lock file
   status "Setting up $env_name environment (this may take a while)..."
-  conda create --file $platform_lock_file --name $env_name 2>&1 | tee "env_install.log"
+  conda create --file $platform_lockfile --name $env_name 2>&1 | tee "env_install.log"
   if ! tr -d \\n < env_install.log | grep -q "Executing transaction: ...working... done"; then
     fail "$env_name environment setup failed"
     echo "Console output has been saved to env_install.log."
@@ -94,15 +98,16 @@ fi
 # Check if os is mac or linux
 if [[ "$OSTYPE" == "darwin"* ]]; then
   success "macOS detected"
+  arch=$(uname -m)  # Support Apple Silicon
   shell=$(basename "$(dscl . -read ~/ UserShell | cut -f 2 -d " ")")
-  miniconda_installer="Miniconda3-py${python_version/./}_${miniconda_version}-MacOSX-x86_64.sh"
-  platform_lock_file="./conda/conda-osx-64.lock"
+  miniconda_installer="Miniconda3-py${miniconda_python_version}_${miniconda_version}-MacOSX-${arch}.sh"
+  platform_lockfile="${cwd}/conda/conda-osx-64.lock"
   setup_macOS_command_line_tools
 elif [[ "$OSTYPE" == "linux-gnu" ]]; then
   success "Linux detected"
   shell="$(basename "$SHELL")"
-  miniconda_installer="Miniconda3-py${python_version/./}_${miniconda_version}-Linux-x86_64.sh"
-  platform_lock_file="./conda/conda-linux-64.lock"
+  miniconda_installer="Miniconda3-py${miniconda_python_version}_${miniconda_version}-Linux-x86_64.sh"
+  platform_lockfile="${cwd}/conda/conda-linux-64.lock"
 else
   fail "Unsupported OS"
   exit 1
@@ -112,6 +117,7 @@ fi
 if grep -q "conda init" ~/."$shell"rc ~/."$shell"_profile 2> /dev/null; then
   success "Conda is already installed for $shell"
   eval "$(conda shell."$shell" hook)"
+  miniconda_installed=0
 else
   status "Downloading Miniconda..."
   curl -O -# https://repo.anaconda.com/miniconda/$miniconda_installer
@@ -119,7 +125,8 @@ else
     success "Miniconda downloaded"
     verify_conda_checksum $miniconda_installer
     status "Running interactive Miniconda installer..."
-    if ! $shell $miniconda_installer; then
+    # Use bash since the installer appears to no longer work with zsh
+    if ! bash $miniconda_installer; then
       fail "Miniconda installation failed"
       exit 1
     fi
@@ -134,6 +141,7 @@ else
   conda config --set auto_activate_base false
 
   success "Miniconda installed"
+  miniconda_installed=1
   rm $miniconda_installer
 fi
 
@@ -141,29 +149,22 @@ fi
 if conda env list | grep -q "^${env_name}\s"; then
   echo
   echo "The Conda environment $env_name already exists."
-  echo "    1) Update environment"
-  echo "    2) Remove and recreate environment"
+  echo "It must be removed and recreated."
   echo
-  read -p "Select an option [1/2]: " -n 1 -r
+  read -p "Would you like to proceed? [y/n]: " -n 1 -r
 
-  if [[ $REPLY =~ ^[1]$ ]]; then
-    echo
-    echo
-    status "Updating $env_name environment..."
-    conda update --file $platform_lock_file --name "$env_name" 2>&1 | tee "env_update.log"
-    if ! tr -d \\n < env_install.log | grep -q "Executing transaction: ...working... done"; then
-      fail "Failed to update the environment"
-      echo "Check the env_update.log file for more information."
-      exit 1
-    fi
-    success "$env_name environment updated"
-  elif [[ $REPLY =~ ^[2]$ ]]; then
+  if [[ $REPLY =~ ^y$ ]]; then
     echo
     echo
     status "Removing $env_name environment..."
     conda env remove -n "$env_name" -y > /dev/null 2>&1
     success "Environment removed"
     setup_environment
+  elif [[ $REPLY =~ ^n$ ]]; then
+    echo
+    echo
+    fail "Exiting..."
+    exit 1
   else
     echo
     fail "Invalid option: $REPLY"
@@ -180,7 +181,7 @@ conda env config vars set PYTHONNOUSERSITE=1 > /dev/null  # FYI: cannot be set b
 
 # Install the tinyRNA codebase
 status "Installing tinyRNA codebase via pip..."
-if ! pip install . > "pip_install.log" 2>&1; then
+if ! pip install "$cwd" > "pip_install.log" 2>&1; then
   fail "Failed to install tinyRNA codebase"
   echo "Check the pip_install.log file for more information."
   exit 1
@@ -188,6 +189,12 @@ fi
 success "tinyRNA codebase installed"
 
 success "Setup complete"
+if [[ $miniconda_installed -eq 1 ]]; then
+  status "First, run this one-time command to finalize the Miniconda installation:"
+  echo
+  echo "  source ~/${shell}.rc"
+  echo
+fi
 status "To activate the environment, run:"
 echo
 echo "  conda activate $env_name"

From 08162697ff184a2b66e24d5716e357c333daaf58 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 15:13:59 -0700
Subject: [PATCH 20/22] Removing unused imports in resume.py

---
 tiny/rna/resume.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tiny/rna/resume.py b/tiny/rna/resume.py
index 24858947..549f0b51 100644
--- a/tiny/rna/resume.py
+++ b/tiny/rna/resume.py
@@ -2,9 +2,7 @@
 import re
 import sys
 
-import ruamel.yaml
 from ruamel.yaml.comments import CommentedOrderedMap
-from pkg_resources import resource_filename
 from abc import ABC, abstractmethod
 from glob import glob
 

From 637fdae5a770cfb0684770d5852f36d238d1b26e Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 15:15:05 -0700
Subject: [PATCH 21/22] Minor logical change in the functions that set up
 command line args in entry.py

---
 tiny/entry.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tiny/entry.py b/tiny/entry.py
index 1b25e45b..d7d6ce09 100644
--- a/tiny/entry.py
+++ b/tiny/entry.py
@@ -63,8 +63,8 @@ def add_subcommand(command, brief, detail, config: str = None, **kwargs):
             args_section = parser.add_argument_group("Required arguments")
             args_section.add_argument(
                 '--config',
-                help=f"The file path to your {config.replace('_', ' ')}",
-                metavar=config.upper(),
+                help=f"The file path to your {config}",
+                metavar=config.upper().replace(' ', '_'),
                 required=True
             )
 
@@ -94,7 +94,7 @@ def priority_sort(x):
                "file: the Paths File. Within the Paths File you must specify the location "
                "of your file inputs, including two final configuration files: the Samples "
                "Sheet and Features Sheet.",
-        config='run_config',
+        config='Run Config',
         formatter_class=SmartFormatter
     )
 
@@ -108,14 +108,14 @@ def priority_sort(x):
         "recount",
         brief="Resume an analysis at the tiny-count step",
         detail=resume_helpstring_template.format(step_name='tiny-count'),
-        config='processed_run_config'
+        config='Processed Run Config'
     )
 
     add_subcommand(
         "replot",
         brief="Resume an analysis at the tiny-plot step",
         detail=resume_helpstring_template.format(step_name='tiny-plot'),
-        config='processed_run_config'
+        config='Processed Run Config'
     )
 
     add_subcommand(
@@ -126,7 +126,7 @@ def priority_sort(x):
                "Run Config, and it will copy the workflow CWL files to the current "
                'directory. You can also pass the word "none" for your Run Config to '
                "skip processing and only copy the workflow files.",
-        config='run_config'
+        config='Run Config'
     )
 
     return primary_parser.parse_args()

From 1caed14ad355a95df9cb8cbb9a854756c90e3bfc Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 24 May 2023 15:18:07 -0700
Subject: [PATCH 22/22] Switching to a safer usage of subprocess.run() for
 calling cwltool

---
 tiny/entry.py | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/tiny/entry.py b/tiny/entry.py
index d7d6ce09..6660da41 100644
--- a/tiny/entry.py
+++ b/tiny/entry.py
@@ -233,17 +233,18 @@ def run_cwltool_subprocess(config_object: 'ConfigBase', workflow: str, run_direc
     parallel = config_object['run_parallel']
     verbosity = config_object['verbosity']
 
-    command = ['cwltool --timestamps --relax-path-checks --on-error continue']
-    command.append(f'--log-dir {run_directory}/{config_object["dir_name_logs"]}')
-    command.append(f'--outdir {run_directory}')
-
-    if tmpdir is not None: command.append(f'--tmpdir-prefix {tmpdir}')
-    if verbosity == 'debug': command.append('--debug --js-console --leave-tmpdir')
-    if verbosity == 'quiet': command.append('--quiet')
-    if parallel: command.append('--parallel')
-
-    cwl_runner = ' '.join(command + [workflow, processed_configfile])
-    return subprocess.run(cwl_runner, shell=True).returncode
+    command = ["cwltool",
+               "--timestamps", "--relax-path-checks", "--on-error", "continue",
+               "--log-dir", os.path.join(run_directory, config_object['dir_name_logs']),
+               "--outdir", run_directory]
+
+    if tmpdir is not None: command.extend(["--tmpdir-prefix", tmpdir])
+    if verbosity == 'debug': command.extend(["--debug", "--js-console", "--leave-tmpdir"])
+    if verbosity == 'quiet': command.append("--quiet")
+    if parallel: command.append("--parallel")
+
+    command.extend([workflow, processed_configfile])
+    return subprocess.run(command).returncode
 
 
 def run_cwltool_native(config_object: 'ConfigBase', workflow: str, run_directory: str = '.') -> int: