From 17f3fd600173218c343b98bc3b21bb093274a9db Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Tue, 9 Nov 2021 15:27:40 -0600 Subject: [PATCH 01/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 34 +++++++++------------------------- etc/requirements.full.pip.txt | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+), 25 deletions(-) create mode 100644 etc/requirements.full.pip.txt diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1b3374691d..96bdf813a2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,7 +8,6 @@ on: - master - develop - 'release*' - - 'ci-pytest' pull_request: branches: [master, develop] @@ -116,7 +115,7 @@ jobs: test-path: run_scripts.py defaults: run: - shell: bash -l {0} + shell: bash steps: # check out repo @@ -126,35 +125,20 @@ jobs: - name: Get branch name uses: nelonoel/branch-name@v1.0.1 - - name: Cache Miniconda - uses: actions/cache@v2.1.0 - env: - # Increase this value to reset cache if environment.yml has changed - CACHE_NUMBER: 2 - with: - path: ~/conda_pkgs_dir - key: ${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.run-type }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('etc/environment.yml') }} - - # Standard python fails on windows without GDAL installation - # Using custom bash shell ("shell: bash -l {0}") with Miniconda - - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v2.1.1 + - name: Setup Python + uses: actions/setup-python@v2.2.2 with: python-version: ${{ matrix.python-version }} - mamba-version: "*" - channels: conda-forge - auto-update-conda: true - activate-environment: flopy - use-only-tar-bz2: true - - name: Add jupyter and jupytext to notebooks run - if: matrix.run-type == 'nb' + - name: Install Python packages run: | - mamba install --name flopy jupyter jupytext + python -m pip install --upgrade pip + pip install -r etc/requirements.full.pip.txt - - name: Add packages to flopy environment using mamba or conda + - name: Add jupyter and jupytext to notebooks run + if: matrix.run-type == 'nb' run: | - mamba env update --name flopy --file etc/environment.yml + pip install jupyter jupytext - name: Install pymake, xmipy, and flopy run: | diff --git a/etc/requirements.full.pip.txt b/etc/requirements.full.pip.txt new file mode 100644 index 0000000000..941c07ab98 --- /dev/null +++ b/etc/requirements.full.pip.txt @@ -0,0 +1,34 @@ +matplotlib>=1.4.0 +numpy>=1.15.0 + +# testing +pylint +flake8 +black +coverage +pytest +pytest-xdist +pytest-cov + +# optional +appdirs +python-dateutil>=2.4.0 +affine +scipy +pandas +netcdf4 +pyshp>=2.0.0 +rasterio +fiona +descartes +pyproj +shapely +geos +geojson +vtk + +# external dependencies +requests + +# MODFLOW API dependencies +bmipy From c1cd7b1ce2c9307842969a3510caa0bffb09693e Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Tue, 9 Nov 2021 16:12:50 -0600 Subject: [PATCH 02/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 96bdf813a2..ca072f452b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -130,9 +130,19 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install Python packages + - name: Upgrade pip run: | python -m pip install --upgrade pip + + - name: Install GDAL on Windows + if: runner.os == 'Windows' + run: | + pip install gohlkegrabber + ggrab c:\temp gdal + pip install c:\temp\GDAL-3.3.3-cp310-cp310-win_amd64.whl + + - name: Install Python packages + run: | pip install -r etc/requirements.full.pip.txt - name: Add jupyter and jupytext to notebooks run From 16967cbad492fe30a2c2be8e40f2daa1ce41783a Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Tue, 9 Nov 2021 16:21:39 -0600 Subject: [PATCH 03/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ca072f452b..7b9ef8e125 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -138,8 +138,8 @@ jobs: if: runner.os == 'Windows' run: | pip install gohlkegrabber - ggrab c:\temp gdal - pip install c:\temp\GDAL-3.3.3-cp310-cp310-win_amd64.whl + ggrab c:\\temp gdal + pip install --no-index --find-links=c:\\temp - name: Install Python packages run: | From 5ad936121fc099bc7c8f793ba31629a056e5e3e8 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Tue, 9 Nov 2021 16:29:39 -0600 Subject: [PATCH 04/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7b9ef8e125..1e32b40c4f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -138,8 +138,8 @@ jobs: if: runner.os == 'Windows' run: | pip install gohlkegrabber - ggrab c:\\temp gdal - pip install --no-index --find-links=c:\\temp + ggrab -v=3.3.3 c:\\temp gdal + pip install c:\\temp\GDAL-3.3.3-cp310-cp310-win_amd64.whl - name: Install Python packages run: | From ba46d23e6f7ebcf9683ef39a7562f5674997d50b Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Tue, 9 Nov 2021 16:36:06 -0600 Subject: [PATCH 05/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1e32b40c4f..2756afa12d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -139,7 +139,7 @@ jobs: run: | pip install gohlkegrabber ggrab -v=3.3.3 c:\\temp gdal - pip install c:\\temp\GDAL-3.3.3-cp310-cp310-win_amd64.whl + pip install c:\\temp\\GDAL-3.3.3-cp310-cp310-win_amd64.whl - name: Install Python packages run: | From 71f51e30c314af66714899c8af90c4fcc14f9405 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Tue, 9 Nov 2021 16:46:27 -0600 Subject: [PATCH 06/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 2 +- .github/workflows/rtd.yml | 22 ++++++++++------------ 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2756afa12d..502a4982ac 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -139,7 +139,7 @@ jobs: run: | pip install gohlkegrabber ggrab -v=3.3.3 c:\\temp gdal - pip install c:\\temp\\GDAL-3.3.3-cp310-cp310-win_amd64.whl + pip install c:\\temp\\GDAL-3.3.3-cp39-cp39-win_amd64.whl - name: Install Python packages run: | diff --git a/.github/workflows/rtd.yml b/.github/workflows/rtd.yml index b02da360e8..34b5c6ea5b 100644 --- a/.github/workflows/rtd.yml +++ b/.github/workflows/rtd.yml @@ -32,24 +32,22 @@ jobs: echo $GITHUB_REF echo $GITHUB_EVENT_NAME - # Standard python fails on windows without GDAL installation - # Using custom bash shell ("shell: bash -l {0}") with Miniconda - - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v2.1.1 + - name: Setup Python + uses: actions/setup-python@v2.2.2 with: python-version: 3.9 - mamba-version: "*" - channels: conda-forge - auto-update-conda: true - activate-environment: flopy - - name: Add jupyter and jupytext to scripts run + - name: Upgrade pip + run: | + python -m pip install --upgrade pip + + - name: Install Python packages run: | - mamba install --name flopy jupyter jupytext + pip install -r etc/requirements.full.pip.txt - - name: Add packages to flopy environment + - name: Add jupyter and jupytext to scripts run run: | - mamba env update --name flopy --file etc/environment.yml + pip install jupyter jupytext - name: Install pymake, xmipy, and flopy run: | From 8aa0d6ccb37ef7658d0593f7559c2f774d95ec98 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 09:10:29 -0600 Subject: [PATCH 07/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 25 +++++++++++++++++++---- etc/requirements.windows.pip.txt | 35 ++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+), 4 deletions(-) create mode 100644 etc/requirements.windows.pip.txt diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 502a4982ac..8d7db43f90 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -134,17 +134,34 @@ jobs: run: | python -m pip install --upgrade pip - - name: Install GDAL on Windows + - name: Install Python packages on Windows if: runner.os == 'Windows' run: | - pip install gohlkegrabber - ggrab -v=3.3.3 c:\\temp gdal + pip install -r etc/requirements.windows.pip.txt + ggrab c:\\temp gdal + ggrab c:\\temp rasterio pip install c:\\temp\\GDAL-3.3.3-cp39-cp39-win_amd64.whl - - name: Install Python packages + - name: Install Python packages on Linux and MacOS + if: runner.os != 'Windows' run: | pip install -r etc/requirements.full.pip.txt + - name: Install Python packages with GDAL dependencies on windows + if: runner.os == 'Windows' + shell: python + run: | + import os, glob, pip + from gohlkegrabber import GohlkeGrabber + gg = GohlkeGrabber() + wheel_path = os.path.join(".", "wheels") + gg.retrieve(wheel_path, "rasterio'") + gg.retrieve(wheel_path, "fiona") + gg.retrieve(wheel_path, "gdal") + glob_str = os.path.join(wheel_path, "*.whl") + for path in glob.glob(glob_str): + pip.main(['install', path]) + - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' run: | diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt new file mode 100644 index 0000000000..5c4863f995 --- /dev/null +++ b/etc/requirements.windows.pip.txt @@ -0,0 +1,35 @@ +matplotlib>=1.4.0 +numpy>=1.15.0 + +# testing +pylint +flake8 +black +coverage +pytest +pytest-xdist +pytest-cov + +# optional +appdirs +python-dateutil>=2.4.0 +affine +scipy +pandas +netcdf4 +pyshp>=2.0.0 +descartes +pyproj +shapely +geos +geojson +vtk + +# external dependencies +requests + +# MODFLOW API dependencies +bmipy + +# golke installer +gohlkegrabber From 154a945b61392fd67b6238f6a2b5280debbb3b04 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 09:17:18 -0600 Subject: [PATCH 08/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8d7db43f90..eed53e85d9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -138,9 +138,6 @@ jobs: if: runner.os == 'Windows' run: | pip install -r etc/requirements.windows.pip.txt - ggrab c:\\temp gdal - ggrab c:\\temp rasterio - pip install c:\\temp\\GDAL-3.3.3-cp39-cp39-win_amd64.whl - name: Install Python packages on Linux and MacOS if: runner.os != 'Windows' From 3cc72ae7d938deb5a3641c42255def95e4fd19b6 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 09:36:03 -0600 Subject: [PATCH 09/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index eed53e85d9..2a391c3211 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -152,12 +152,13 @@ jobs: from gohlkegrabber import GohlkeGrabber gg = GohlkeGrabber() wheel_path = os.path.join(".", "wheels") - gg.retrieve(wheel_path, "rasterio'") + os.makedirs(wheel_path, exist_ok=True) + gg.retrieve(wheel_path, "rasterio") gg.retrieve(wheel_path, "fiona") gg.retrieve(wheel_path, "gdal") glob_str = os.path.join(wheel_path, "*.whl") for path in glob.glob(glob_str): - pip.main(['install', path]) + pip.main(["install", path]) - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' From 7fced55ec4030c32f9cc3cae2eac27c37f713356 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 10:58:18 -0600 Subject: [PATCH 10/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 2 +- etc/requirements.windows.pip.txt | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a391c3211..69f39ab022 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -174,7 +174,7 @@ jobs: - name: Prepare for the autotests working-directory: ./autotest run: | - pytest -v ci_prepare.py + python ci_prepare.py - name: Add executables directory to path run: | diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index 5c4863f995..bce37812fb 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -31,5 +31,6 @@ requests # MODFLOW API dependencies bmipy -# golke installer +# for golke installer +wheel gohlkegrabber From ab2367aa1593f7f91499b1c6cb4a825d645638b5 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 11:16:12 -0600 Subject: [PATCH 11/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 69f39ab022..ecf0a270cd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -115,7 +115,7 @@ jobs: test-path: run_scripts.py defaults: run: - shell: bash + shell: bash -l {0} steps: # check out repo @@ -144,7 +144,7 @@ jobs: run: | pip install -r etc/requirements.full.pip.txt - - name: Install Python packages with GDAL dependencies on windows + - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' shell: python run: | @@ -153,12 +153,14 @@ jobs: gg = GohlkeGrabber() wheel_path = os.path.join(".", "wheels") os.makedirs(wheel_path, exist_ok=True) + gg.retrieve(wheel_path, "gdal") gg.retrieve(wheel_path, "rasterio") gg.retrieve(wheel_path, "fiona") - gg.retrieve(wheel_path, "gdal") - glob_str = os.path.join(wheel_path, "*.whl") - for path in glob.glob(glob_str): - pip.main(["install", path]) + + - name: Install Python packages with GDAL dependencies on Windows + if: runner.os == 'Windows' + run: | + pip install --no-index --find-links=wheels/ - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' @@ -174,7 +176,7 @@ jobs: - name: Prepare for the autotests working-directory: ./autotest run: | - python ci_prepare.py + pytest -v ci_prepare.py - name: Add executables directory to path run: | From 6d42973a9d46cad0854cbfea278fedc5f459f78a Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 12:08:38 -0600 Subject: [PATCH 12/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ecf0a270cd..1f3682d96e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -115,7 +115,7 @@ jobs: test-path: run_scripts.py defaults: run: - shell: bash -l {0} + shell: bash steps: # check out repo @@ -182,6 +182,12 @@ jobs: run: | echo "$HOME/.local/bin" >> $GITHUB_PATH + - name: Write PATH and list the contents of $HOME/.local/bin + run: | + $PATH + ls $HOME/.local/bin + which mf6 + - name: Run pytest on autotest scripts if: matrix.run-type == 'std' working-directory: ./autotest From 9313cca34e81c104993165071c0f11fc66cfd4fe Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 12:21:19 -0600 Subject: [PATCH 13/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1f3682d96e..532153377c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -160,7 +160,9 @@ jobs: - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' run: | - pip install --no-index --find-links=wheels/ + pip install --find-links=file:///wheels gdal + pip install --find-links=file:///wheels rasterio + pip install --find-links=file:///wheels fiona - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' @@ -182,12 +184,6 @@ jobs: run: | echo "$HOME/.local/bin" >> $GITHUB_PATH - - name: Write PATH and list the contents of $HOME/.local/bin - run: | - $PATH - ls $HOME/.local/bin - which mf6 - - name: Run pytest on autotest scripts if: matrix.run-type == 'std' working-directory: ./autotest From 9c419c1b710821ba476029e3233a19bd69b2ee5c Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 15:48:51 -0600 Subject: [PATCH 14/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 532153377c..2a16a66611 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -160,9 +160,9 @@ jobs: - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' run: | - pip install --find-links=file:///wheels gdal - pip install --find-links=file:///wheels rasterio - pip install --find-links=file:///wheels fiona + pip install --no-index --find-links=./wheels/ gdal + pip install --no-index --find-links=./wheels/ rasterio + pip install --no-index --find-links=./wheels/ fiona - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' From 5ecf27731236acedef0bcad52b63cd73f69ceaa5 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 16:06:51 -0600 Subject: [PATCH 15/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 3 ++- etc/requirements.windows.pip.txt | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a16a66611..f7a039fe62 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -148,7 +148,7 @@ jobs: if: runner.os == 'Windows' shell: python run: | - import os, glob, pip + import os from gohlkegrabber import GohlkeGrabber gg = GohlkeGrabber() wheel_path = os.path.join(".", "wheels") @@ -160,6 +160,7 @@ jobs: - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' run: | + ls -lh ./wheels/ pip install --no-index --find-links=./wheels/ gdal pip install --no-index --find-links=./wheels/ rasterio pip install --no-index --find-links=./wheels/ fiona diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index bce37812fb..eee3fd8024 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -34,3 +34,5 @@ bmipy # for golke installer wheel gohlkegrabber +cligj>=0.5 +click-plugins From eb498e376b8f52ab70af80fda2fc7924eefd4104 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 16:23:57 -0600 Subject: [PATCH 16/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 11 ++++++----- etc/requirements.windows.pip.txt | 6 +++++- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f7a039fe62..90e9a72a99 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -130,9 +130,10 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Upgrade pip + - name: Upgrade pip and install wheel run: | python -m pip install --upgrade pip + pip install wheel - name: Install Python packages on Windows if: runner.os == 'Windows' @@ -153,17 +154,17 @@ jobs: gg = GohlkeGrabber() wheel_path = os.path.join(".", "wheels") os.makedirs(wheel_path, exist_ok=True) - gg.retrieve(wheel_path, "gdal") + gg.retrieve(wheel_path, "GDAL") gg.retrieve(wheel_path, "rasterio") - gg.retrieve(wheel_path, "fiona") + gg.retrieve(wheel_path, "Fiona") - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' run: | ls -lh ./wheels/ - pip install --no-index --find-links=./wheels/ gdal + pip install --no-index --find-links=./wheels/ GDAL pip install --no-index --find-links=./wheels/ rasterio - pip install --no-index --find-links=./wheels/ fiona + pip install --no-index --find-links=./wheels/ Fiona - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index eee3fd8024..91ea400878 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -32,7 +32,11 @@ requests bmipy # for golke installer -wheel gohlkegrabber +attrs +certifi +click>=4.0 cligj>=0.5 +snuggs>=1.4.1 click-plugins +setuptools From d48c2d579333ac39d544421d8062f9b9dbc74e9c Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 16:31:20 -0600 Subject: [PATCH 17/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 90e9a72a99..929110feb6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -100,7 +100,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-latest, windows-latest] + os: [windows-latest] python-version: [3.9, 3.8, 3.7] run-type: [std] test-pth: [""] @@ -154,9 +154,9 @@ jobs: gg = GohlkeGrabber() wheel_path = os.path.join(".", "wheels") os.makedirs(wheel_path, exist_ok=True) - gg.retrieve(wheel_path, "GDAL") + gg.retrieve(wheel_path, "gdal") gg.retrieve(wheel_path, "rasterio") - gg.retrieve(wheel_path, "Fiona") + gg.retrieve(wheel_path, "fiona") - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' From c5ca45cd64ce3800afcaca1d436f5db8b72dfab7 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 16:45:16 -0600 Subject: [PATCH 18/28] ci: switch from conda to standard python and pip --- etc/requirements.windows.pip.txt | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index 91ea400878..27e46f76ee 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -31,12 +31,16 @@ requests # MODFLOW API dependencies bmipy -# for golke installer +# golke installer gohlkegrabber -attrs + +# dependencies for rasterio and Fiona +attrs>=17 certifi click>=4.0 cligj>=0.5 snuggs>=1.4.1 -click-plugins +click-plugins>=1.0 +six>=1.7 +munch setuptools From d38ca3a893299af8a29d0f37422e093849243695 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 17:00:43 -0600 Subject: [PATCH 19/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 9 +++++---- etc/requirements.windows.pip.txt | 20 ++++++++++---------- 2 files changed, 15 insertions(+), 14 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 929110feb6..49154f362f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -145,7 +145,7 @@ jobs: run: | pip install -r etc/requirements.full.pip.txt - - name: Install Python packages with GDAL dependencies on Windows + - name: Download Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' shell: python run: | @@ -162,9 +162,9 @@ jobs: if: runner.os == 'Windows' run: | ls -lh ./wheels/ - pip install --no-index --find-links=./wheels/ GDAL - pip install --no-index --find-links=./wheels/ rasterio - pip install --no-index --find-links=./wheels/ Fiona + pip install --find-links=./wheels/ gdal + pip install --find-links=./wheels/ rasterio + pip install --find-links=./wheels/ fiona - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' @@ -190,6 +190,7 @@ jobs: if: matrix.run-type == 'std' working-directory: ./autotest run: | + echo "$PATH" pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - name: Run pytest on scripts and notebooks diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index 27e46f76ee..a6e0484ad0 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -34,13 +34,13 @@ bmipy # golke installer gohlkegrabber -# dependencies for rasterio and Fiona -attrs>=17 -certifi -click>=4.0 -cligj>=0.5 -snuggs>=1.4.1 -click-plugins>=1.0 -six>=1.7 -munch -setuptools +# # dependencies for rasterio and Fiona +# attrs>=17 +# certifi +# click>=4.0 +# cligj>=0.5 +# snuggs>=1.4.1 +# click-plugins>=1.0 +# six>=1.7 +# munch +# setuptools From 9aca4127e7f883f584112309a40c9fb15caabba2 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 17:15:09 -0600 Subject: [PATCH 20/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 7 ++++--- etc/requirements.windows.pip.txt | 20 ++++++++++---------- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 49154f362f..e7759e803c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -162,9 +162,10 @@ jobs: if: runner.os == 'Windows' run: | ls -lh ./wheels/ - pip install --find-links=./wheels/ gdal - pip install --find-links=./wheels/ rasterio - pip install --find-links=./wheels/ fiona + for x in `ls -tr ./wheels/`; do pip install $x; done +# pip install --no-index --find-links=./wheels/ gdal +# pip install --no-index --find-links=./wheels/ rasterio +# pip install --no-index --find-links=./wheels/ fiona - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index a6e0484ad0..27e46f76ee 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -34,13 +34,13 @@ bmipy # golke installer gohlkegrabber -# # dependencies for rasterio and Fiona -# attrs>=17 -# certifi -# click>=4.0 -# cligj>=0.5 -# snuggs>=1.4.1 -# click-plugins>=1.0 -# six>=1.7 -# munch -# setuptools +# dependencies for rasterio and Fiona +attrs>=17 +certifi +click>=4.0 +cligj>=0.5 +snuggs>=1.4.1 +click-plugins>=1.0 +six>=1.7 +munch +setuptools From 89ec2effc4cae5c18e53f09fdc5c009263d7a843 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 17:24:30 -0600 Subject: [PATCH 21/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e7759e803c..f20ade8006 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -161,8 +161,10 @@ jobs: - name: Install Python packages with GDAL dependencies on Windows if: runner.os == 'Windows' run: | - ls -lh ./wheels/ - for x in `ls -tr ./wheels/`; do pip install $x; done + ls -ltr ./wheels/ + pip install ./wheels/GDAL* + pip install ./wheels/rasterio* + pip install ./wheels/Fiona* # pip install --no-index --find-links=./wheels/ gdal # pip install --no-index --find-links=./wheels/ rasterio # pip install --no-index --find-links=./wheels/ fiona From 222390298e90998f60eff6ca4c92d0363fa39d95 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 17:47:53 -0600 Subject: [PATCH 22/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f20ade8006..4016386aba 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -100,11 +100,19 @@ jobs: strategy: fail-fast: false matrix: - os: [windows-latest] - python-version: [3.9, 3.8, 3.7] + os: [ubuntu-latest] + python-version: [3.10, 3.9, 3.8, 3.7] run-type: [std] test-pth: [""] include: + - os: macos-latest + python-version: 3.9 + run-type: std + test-path: "" + - os: windows-latest + python-version: 3.9 + run-type: std + test-path: "" - os: ubuntu-latest python-version: 3.9 run-type: nb @@ -165,9 +173,6 @@ jobs: pip install ./wheels/GDAL* pip install ./wheels/rasterio* pip install ./wheels/Fiona* -# pip install --no-index --find-links=./wheels/ gdal -# pip install --no-index --find-links=./wheels/ rasterio -# pip install --no-index --find-links=./wheels/ fiona - name: Add jupyter and jupytext to notebooks run if: matrix.run-type == 'nb' @@ -188,12 +193,19 @@ jobs: - name: Add executables directory to path run: | echo "$HOME/.local/bin" >> $GITHUB_PATH + echo "$PATH" - - name: Run pytest on autotest scripts - if: matrix.run-type == 'std' + - name: Run pytest on autotest scripts on MacOS and Linux + if: matrix.run-type == 'std' && runner.os != 'Windows' + working-directory: ./autotest + run: | + pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml + + - name: Run pytest on autotest scripts on Windows + if: matrix.run-type == 'std' && runner.os == 'Windows' + shell: pwsh working-directory: ./autotest run: | - echo "$PATH" pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - name: Run pytest on scripts and notebooks From 560057e609cf4fe95c7c627e0b931fe10ba6ca63 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Wed, 10 Nov 2021 18:45:24 -0600 Subject: [PATCH 23/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4016386aba..b5fba6c2f6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -55,7 +55,6 @@ jobs: run: shell: bash - if: github.event_name != 'schedule' steps: # check out repo - name: Checkout flopy repo @@ -101,7 +100,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: [3.10, 3.9, 3.8, 3.7] + python-version: [3.9, 3.8, 3.7] run-type: [std] test-pth: [""] include: @@ -193,17 +192,14 @@ jobs: - name: Add executables directory to path run: | echo "$HOME/.local/bin" >> $GITHUB_PATH - echo "$PATH" - - name: Run pytest on autotest scripts on MacOS and Linux - if: matrix.run-type == 'std' && runner.os != 'Windows' - working-directory: ./autotest + - name: Output HOME directory and path run: | - pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml + echo "$HOME" + echo "$PATH" - - name: Run pytest on autotest scripts on Windows - if: matrix.run-type == 'std' && runner.os == 'Windows' - shell: pwsh + - name: Run pytest on autotest scripts + if: matrix.run-type == 'std' working-directory: ./autotest run: | pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml From 89daf25ed513e82162b77ece6e236c3b78e8f970 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Thu, 11 Nov 2021 16:34:50 -0600 Subject: [PATCH 24/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b5fba6c2f6..77b7a3a1e6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -192,10 +192,12 @@ jobs: - name: Add executables directory to path run: | echo "$HOME/.local/bin" >> $GITHUB_PATH + echo "$HOME/.local/bin" >> $PATH - name: Output HOME directory and path run: | echo "$HOME" + echo "$GITHUB_PATH" echo "$PATH" - name: Run pytest on autotest scripts From 1ae3164bd5012cc21cebc8f9ea80cb32155b2dff Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Thu, 11 Nov 2021 17:02:08 -0600 Subject: [PATCH 25/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 77b7a3a1e6..33d138adf3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -192,18 +192,20 @@ jobs: - name: Add executables directory to path run: | echo "$HOME/.local/bin" >> $GITHUB_PATH - echo "$HOME/.local/bin" >> $PATH - - name: Output HOME directory and path + - name: Run pytest on autotest scripts + if: matrix.run-type == 'std' && runner.os != 'Windows' + working-directory: ./autotest run: | - echo "$HOME" echo "$GITHUB_PATH" - echo "$PATH" + pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - - name: Run pytest on autotest scripts - if: matrix.run-type == 'std' + - name: Run pytest on autotest scripts on Windows + if: matrix.run-type == 'std' && runner.os == 'Windows' working-directory: ./autotest + shell: cmd run: | + path pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - name: Run pytest on scripts and notebooks From b8dff808e4b33e2d2b6ffdffebaa12758fdefe34 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Thu, 11 Nov 2021 17:18:30 -0600 Subject: [PATCH 26/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 11 ++++++++--- etc/requirements.windows.pip.txt | 20 ++++++++++---------- 2 files changed, 18 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 33d138adf3..70865b8787 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -189,15 +189,20 @@ jobs: run: | pytest -v ci_prepare.py - - name: Add executables directory to path + - name: Add executables directory to path on Linux and MacOS + if: runner.os != 'Windows' run: | echo "$HOME/.local/bin" >> $GITHUB_PATH - - name: Run pytest on autotest scripts + - name: Add executables directory to path on Windows + if: runner.os == 'Windows' + run: | + echo "C:\Users\runneradmin\.local\bin" >> $GITHUB_PATH + + - name: Run pytest on autotest scripts on Linux and MacOS if: matrix.run-type == 'std' && runner.os != 'Windows' working-directory: ./autotest run: | - echo "$GITHUB_PATH" pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - name: Run pytest on autotest scripts on Windows diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index 27e46f76ee..a6e0484ad0 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -34,13 +34,13 @@ bmipy # golke installer gohlkegrabber -# dependencies for rasterio and Fiona -attrs>=17 -certifi -click>=4.0 -cligj>=0.5 -snuggs>=1.4.1 -click-plugins>=1.0 -six>=1.7 -munch -setuptools +# # dependencies for rasterio and Fiona +# attrs>=17 +# certifi +# click>=4.0 +# cligj>=0.5 +# snuggs>=1.4.1 +# click-plugins>=1.0 +# six>=1.7 +# munch +# setuptools From a94b48acd68f501854d5c774c02e9a7f5b3ff404 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Fri, 12 Nov 2021 09:11:51 -0600 Subject: [PATCH 27/28] ci: switch from conda to standard python and pip --- .github/workflows/ci.yml | 17 ++++------------- etc/requirements.windows.pip.txt | 11 ----------- 2 files changed, 4 insertions(+), 24 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 70865b8787..28d56ed2a9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -99,17 +99,17 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest] + os: [ubuntu-latest, macos-latest] python-version: [3.9, 3.8, 3.7] run-type: [std] test-pth: [""] include: - - os: macos-latest + - os: windows-latest python-version: 3.9 run-type: std test-path: "" - os: windows-latest - python-version: 3.9 + python-version: 3.8 run-type: std test-path: "" - os: ubuntu-latest @@ -199,18 +199,9 @@ jobs: run: | echo "C:\Users\runneradmin\.local\bin" >> $GITHUB_PATH - - name: Run pytest on autotest scripts on Linux and MacOS - if: matrix.run-type == 'std' && runner.os != 'Windows' - working-directory: ./autotest - run: | - pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - - - name: Run pytest on autotest scripts on Windows - if: matrix.run-type == 'std' && runner.os == 'Windows' + - name: Run pytest on autotest scripts working-directory: ./autotest - shell: cmd run: | - path pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml - name: Run pytest on scripts and notebooks diff --git a/etc/requirements.windows.pip.txt b/etc/requirements.windows.pip.txt index a6e0484ad0..5c4863f995 100644 --- a/etc/requirements.windows.pip.txt +++ b/etc/requirements.windows.pip.txt @@ -33,14 +33,3 @@ bmipy # golke installer gohlkegrabber - -# # dependencies for rasterio and Fiona -# attrs>=17 -# certifi -# click>=4.0 -# cligj>=0.5 -# snuggs>=1.4.1 -# click-plugins>=1.0 -# six>=1.7 -# munch -# setuptools From f3924d590aff908c94d1c23c36aab52b51220d0b Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Fri, 12 Nov 2021 09:47:19 -0600 Subject: [PATCH 28/28] ci: switch from conda to standard python and pip --- .github/workflows/ci-mf6.yml | 1 - .github/workflows/ci.yml | 17 +++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci-mf6.yml b/.github/workflows/ci-mf6.yml index 13f7af802d..8df3c45ac2 100644 --- a/.github/workflows/ci-mf6.yml +++ b/.github/workflows/ci-mf6.yml @@ -8,7 +8,6 @@ on: - master - develop - 'release*' - - 'ci-pytest' pull_request: branches: [master, develop] diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 28d56ed2a9..0963d2412e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -104,14 +104,6 @@ jobs: run-type: [std] test-pth: [""] include: - - os: windows-latest - python-version: 3.9 - run-type: std - test-path: "" - - os: windows-latest - python-version: 3.8 - run-type: std - test-path: "" - os: ubuntu-latest python-version: 3.9 run-type: nb @@ -120,6 +112,14 @@ jobs: python-version: 3.9 run-type: script test-path: run_scripts.py + - os: windows-latest + python-version: 3.9 + run-type: std + test-path: "" + - os: windows-latest + python-version: 3.8 + run-type: std + test-path: "" defaults: run: shell: bash @@ -200,6 +200,7 @@ jobs: echo "C:\Users\runneradmin\.local\bin" >> $GITHUB_PATH - name: Run pytest on autotest scripts + if: matrix.run-type == 'std' working-directory: ./autotest run: | pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml