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/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. 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+https://conda.anaconda.org/bioconda/noarch/bioconductor-annotationdbi-1.60.0-r42hdfd78af_0.tar.bz2#c99dc80c410ee2cb813e59eb3c022b00 +https://conda.anaconda.org/bioconda/noarch/bioconductor-annotate-1.76.0-r42hdfd78af_0.tar.bz2#c4ff237ef3e3833c2ceabb53978a3850 +https://conda.anaconda.org/bioconda/osx-64/bioconductor-genefilter-1.80.0-r42h238a2e4_0.tar.bz2#84837701e4e335f4b868d8ac32df2d26 +https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.76.0-r42hdfd78af_0.tar.bz2#936274098486d93cdc981f0cfd25aa58 +https://conda.anaconda.org/bioconda/osx-64/bioconductor-deseq2-1.38.0-r42hb890f52_0.tar.bz2#b607d382ee280da2b7e0fa3eebf6adcd diff --git a/conda/env.py b/conda/env.py new file mode 100644 index 00000000..4b7e5294 --- /dev/null +++ b/conda/env.py @@ -0,0 +1,328 @@ +"""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 +import json +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, + "mamba=1.4.2", + "conda-lock=1.4.0", + "jake=3.0.0", + "conda-pack=0.7.0" +] + + +def get_args(): + parser = argparse.ArgumentParser() + subcommands = parser.add_subparsers( + title="Available subcommands", + description=f"Use `python3 {os.path.basename(__file__)} -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 + ) + + 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() + + +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, + "--channel", "conda-forge", + "--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] + + +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}. + + 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 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 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() + redirect_imports(denv) + + if args.command == "new-env": + 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.") + + +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/conda/environment.yml b/conda/environment.yml deleted file mode 100644 index 99f0d099..00000000 --- a/conda/environment.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: tinyrna -channels: - - 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 - # tinyRNA codebase must be installed via pip in root project dir -variables: - - PYTHONNOUSERSITE: 1 \ No newline at end of file diff --git a/conda/environment_3.10.yml b/conda/environment_3.10.yml new file mode 100644 index 00000000..e3f22c51 --- /dev/null +++ b/conda/environment_3.10.yml @@ -0,0 +1,27 @@ +name: tinyrna +channels: +- bioconda +- main +dependencies: +- 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 diff --git a/conda/environment_3.9.yml b/conda/environment_3.9.yml new file mode 100644 index 00000000..0f7b025f --- /dev/null +++ b/conda/environment_3.9.yml @@ -0,0 +1,27 @@ +name: tinyrna +channels: +- bioconda +- main +dependencies: +- 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 diff --git a/conda/environment_template.yml b/conda/environment_template.yml new file mode 100644 index 00000000..37cccdac --- /dev/null +++ b/conda/environment_template.yml @@ -0,0 +1,27 @@ +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 the future + - bioconductor-deseq2 + - bowtie + - cython + - fastp + - htseq + - nodejs + - numpy + - pandas + - 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 + - conda-forge::r-base + # tinyRNA codebase must be installed via pip in root project dir +variables: + - PYTHONNOUSERSITE: 1 \ No newline at end of file diff --git a/conda/update-lockfiles.sh b/conda/update-lockfiles.sh deleted file mode 100755 index f2fab3ab..00000000 --- a/conda/update-lockfiles.sh +++ /dev/null @@ -1,79 +0,0 @@ -#!/usr/bin/env bash - -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 environment.yml > "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 - -# Check result for OSX lockfile -check_lockfile_update_status $? \ No newline at end of file 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/setup.sh b/setup.sh index 8834649c..ae9069cc 100755 --- a/setup.sh +++ b/setup.sh @@ -4,10 +4,14 @@ # 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} +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 @@ -134,36 +141,30 @@ else conda config --set auto_activate_base false success "Miniconda installed" + miniconda_installed=1 rm $miniconda_installer 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" - 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" 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/entry.py b/tiny/entry.py index 1b25e45b..6660da41 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() @@ -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}') + 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.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') + 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") - cwl_runner = ' '.join(command + [workflow, processed_configfile]) - return subprocess.run(cwl_runner, shell=True).returncode + command.extend([workflow, processed_configfile]) + return subprocess.run(command).returncode def run_cwltool_native(config_object: 'ConfigBase', workflow: str, run_directory: str = '.') -> int: 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. 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..6bef4819 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])) @@ -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) @@ -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 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 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