From 1d47e171b987a5d4c863b414a834378d41780c18 Mon Sep 17 00:00:00 2001 From: Jose Salvador Jimenez Luna Date: Tue, 11 Oct 2022 15:06:40 +0100 Subject: [PATCH 1/8] deprecate py37 --- .github/workflows/build.yml | 4 ++-- .github/workflows/conda.yml | 4 ++-- conda-recipe/conda_build_config.yaml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0c2d82f..9d5d8e7 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,7 +20,7 @@ jobs: with: activate-environment: delfta environment-file: environment.yml - python-version: 3.7 + python-version: 3.8 auto-activate-base: false - run: | conda info @@ -49,7 +49,7 @@ jobs: with: activate-environment: delfta environment-file: environment_osx.yml - python-version: 3.7 + python-version: 3.8 auto-activate-base: false - run: | conda info diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml index 88ff130..9d151a4 100644 --- a/.github/workflows/conda.yml +++ b/.github/workflows/conda.yml @@ -18,7 +18,7 @@ jobs: activate-environment: delfta environment-file: environment.yml condarc-file: conda-recipe/.condarc - python-version: 3.7 + python-version: 3.8 auto-activate-base: false - run: | conda info @@ -37,7 +37,7 @@ jobs: activate-environment: delfta environment-file: environment_osx.yml condarc-file: conda-recipe/.condarc - python-version: 3.7 + python-version: 3.8 auto-activate-base: false - run: | conda info diff --git a/conda-recipe/conda_build_config.yaml b/conda-recipe/conda_build_config.yaml index 8ac04d6..5a0ba56 100644 --- a/conda-recipe/conda_build_config.yaml +++ b/conda-recipe/conda_build_config.yaml @@ -1,3 +1,3 @@ python: - - 3.7 - 3.8 + - 3.9 From fae0e9c1ae9ca41dee1e8a4b31f3dcc99009960a Mon Sep 17 00:00:00 2001 From: Jose Salvador Jimenez Luna Date: Tue, 11 Oct 2022 15:09:49 +0100 Subject: [PATCH 2/8] update environment file --- environment.yml | 2 +- environment_osx.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index eccd4fb..584bbef 100644 --- a/environment.yml +++ b/environment.yml @@ -10,7 +10,7 @@ dependencies: - numpy=1.19.2 - pandas=1.1.3 - pip=20.2.4 - - python=3.7.4 + - python=3.8 - scikit-learn=0.23.2 - scipy=1.5.2 - tqdm=4.51.0 diff --git a/environment_osx.yml b/environment_osx.yml index 3e2c76f..5d943d4 100644 --- a/environment_osx.yml +++ b/environment_osx.yml @@ -10,7 +10,7 @@ dependencies: - numpy=1.19.2 - pandas=1.1.3 - pip=20.2.4 - - python=3.7.4 + - python=3.8 - scikit-learn=0.23.2 - scipy=1.5.2 - tqdm=4.51.0 From f8542402265044afff4c9073cde090b473e8727d Mon Sep 17 00:00:00 2001 From: Jose Salvador Jimenez Luna Date: Tue, 11 Oct 2022 15:24:37 +0100 Subject: [PATCH 3/8] updated readme and conda meta file --- README.md | 2 +- conda-recipe/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c475c2d..3842220 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ The DelFTa application is an easy-to-use, open-source toolbox for predicting qua ## Installation -While the Linux (and Windows, through WSL) installations fully support GPU-acceleration via cudatoolkit, only CPU inference is currently available under Mac OS. We currently support Python 3.7 and 3.8 builds. +While the Linux (and Windows, through WSL) installations fully support GPU-acceleration via cudatoolkit, only CPU inference is currently available under Mac OS. We currently support Python 3.8 and 3.9 builds. ### Installation via conda diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 9e42e17..8b0b8f3 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: "delfta" - version: "1.0.0" + version: "1.0.1" source: path: ../ From f6b98bcf552dee1dd0aef3ff49384b7b658b964c Mon Sep 17 00:00:00 2001 From: Jose Jimenez-Luna Date: Tue, 11 Oct 2022 17:42:37 +0100 Subject: [PATCH 4/8] tests running for py38 py39 --- .github/workflows/build.yml | 10 +++++++++- environment.yml | 1 - environment_osx.yml | 1 - 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9d5d8e7..0c45e26 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -11,16 +11,20 @@ on: jobs: linux: runs-on: "ubuntu-latest" + strategy: + matrix: + python-version: ['3.8', '3.9'] defaults: run: shell: bash -l {0} + name: py ${{ matrix.python-version }} tests steps: - uses: actions/checkout@v2 - uses: conda-incubator/setup-miniconda@v2 with: activate-environment: delfta environment-file: environment.yml - python-version: 3.8 + python-version: ${{ matrix.python-version }} auto-activate-base: false - run: | conda info @@ -40,9 +44,13 @@ jobs: macos: runs-on: "macos-latest" + strategy: + matrix: + python-version: ['3.8', '3.9'] defaults: run: shell: bash -l {0} + name: py ${{ matrix.python-version }} tests steps: - uses: actions/checkout@v2 - uses: conda-incubator/setup-miniconda@v2 diff --git a/environment.yml b/environment.yml index 584bbef..aac09d7 100644 --- a/environment.yml +++ b/environment.yml @@ -10,7 +10,6 @@ dependencies: - numpy=1.19.2 - pandas=1.1.3 - pip=20.2.4 - - python=3.8 - scikit-learn=0.23.2 - scipy=1.5.2 - tqdm=4.51.0 diff --git a/environment_osx.yml b/environment_osx.yml index 5d943d4..8616d67 100644 --- a/environment_osx.yml +++ b/environment_osx.yml @@ -10,7 +10,6 @@ dependencies: - numpy=1.19.2 - pandas=1.1.3 - pip=20.2.4 - - python=3.8 - scikit-learn=0.23.2 - scipy=1.5.2 - tqdm=4.51.0 From fecfa398d66a2e73eaee0e3bdd4a8e6cfaee11da Mon Sep 17 00:00:00 2001 From: Jose Jimenez-Luna Date: Tue, 11 Oct 2022 17:50:12 +0100 Subject: [PATCH 5/8] version matrix for os x --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0c45e26..731d101 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -57,7 +57,7 @@ jobs: with: activate-environment: delfta environment-file: environment_osx.yml - python-version: 3.8 + python-version: ${{ matrix.python-version }} auto-activate-base: false - run: | conda info From fd76c5a931ce8b4af4940f854c224d4b2ee168e7 Mon Sep 17 00:00:00 2001 From: Jose Jimenez-Luna Date: Tue, 11 Oct 2022 17:59:54 +0100 Subject: [PATCH 6/8] added readthedocs file --- docs/.readthedocs.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/.readthedocs.yaml diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml new file mode 100644 index 0000000..db1fd80 --- /dev/null +++ b/docs/.readthedocs.yaml @@ -0,0 +1,9 @@ +version: 2 + +build: + os: "ubuntu-20.04" + tools: + python: "mambaforge-4.10" + +conda: + environment: environment.yml From f07386a613a25e0bbf02494613c716ce23d6d8ac Mon Sep 17 00:00:00 2001 From: Jose Jimenez-Luna Date: Tue, 11 Oct 2022 18:21:36 +0100 Subject: [PATCH 7/8] different linux and os x build names --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 731d101..5e6c542 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -17,7 +17,7 @@ jobs: defaults: run: shell: bash -l {0} - name: py ${{ matrix.python-version }} tests + name: Linux py ${{ matrix.python-version }} tests steps: - uses: actions/checkout@v2 - uses: conda-incubator/setup-miniconda@v2 @@ -50,7 +50,7 @@ jobs: defaults: run: shell: bash -l {0} - name: py ${{ matrix.python-version }} tests + name: OS X py ${{ matrix.python-version }} tests steps: - uses: actions/checkout@v2 - uses: conda-incubator/setup-miniconda@v2 From 56fba5c60e72b294589b82b912577d43dd94f301 Mon Sep 17 00:00:00 2001 From: Jose Jimenez-Luna Date: Tue, 11 Oct 2022 19:01:43 +0100 Subject: [PATCH 8/8] no longer support os x --- .github/workflows/build.yml | 30 ------------------------------ .github/workflows/conda.yml | 25 ++++--------------------- README.md | 2 +- environment_osx.yml | 24 ------------------------ 4 files changed, 5 insertions(+), 76 deletions(-) delete mode 100644 environment_osx.yml diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5e6c542..d8e764c 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -41,33 +41,3 @@ jobs: - run: | pytest --cov=delfta --cov-config=.coveragerc --cov-report=xml tests/ ./codecov -t ${{ secrets.CODECOV_TOKEN }} - - macos: - runs-on: "macos-latest" - strategy: - matrix: - python-version: ['3.8', '3.9'] - defaults: - run: - shell: bash -l {0} - name: OS X py ${{ matrix.python-version }} tests - steps: - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 - with: - activate-environment: delfta - environment-file: environment_osx.yml - python-version: ${{ matrix.python-version }} - auto-activate-base: false - - run: | - conda info - pip install pytest - name: set pythonpath - - run: | - echo "PYTHONPATH=/Users/runner/work/delfta/delfta" >> $GITHUB_ENV - name: download files - - run: | - python delfta/download.py --tests - name: test - - run: | - pytest diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml index 9d151a4..be1d64e 100644 --- a/.github/workflows/conda.yml +++ b/.github/workflows/conda.yml @@ -8,6 +8,9 @@ on: jobs: linux: runs-on: "ubuntu-latest" + strategy: + matrix: + python-version: ['3.8', '3.9'] defaults: run: shell: bash -l {0} @@ -18,29 +21,9 @@ jobs: activate-environment: delfta environment-file: environment.yml condarc-file: conda-recipe/.condarc - python-version: 3.8 + python-version: ${{ matrix.python-version }} auto-activate-base: false - run: | conda info conda install conda-build anaconda-client --yes cd conda-recipe && pkgs=$(conda build . | grep 'TEST START' | awk '{print $3}') && for pkg in $pkgs;do anaconda -t ${{ secrets.CONDA_TOKEN }} upload -u delfta $pkg; done - - macos: - runs-on: "macos-latest" - defaults: - run: - shell: bash -l {0} - steps: - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 - with: - activate-environment: delfta - environment-file: environment_osx.yml - condarc-file: conda-recipe/.condarc - python-version: 3.8 - auto-activate-base: false - - run: | - conda info - conda install conda-build anaconda-client --yes - cd conda-recipe && pkgs=$(conda build . | grep 'TEST START' | awk '{print $3}') && for pkg in $pkgs;do anaconda -t ${{ secrets.CONDA_TOKEN }} upload -u delfta $pkg; done - diff --git a/README.md b/README.md index 3842220..311502d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ The DelFTa application is an easy-to-use, open-source toolbox for predicting qua ## Installation -While the Linux (and Windows, through WSL) installations fully support GPU-acceleration via cudatoolkit, only CPU inference is currently available under Mac OS. We currently support Python 3.8 and 3.9 builds. +We currently only support Python 3.8 and 3.9 Linux builds. ### Installation via conda diff --git a/environment_osx.yml b/environment_osx.yml deleted file mode 100644 index 8616d67..0000000 --- a/environment_osx.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: delfta -channels: - - pytorch - - defaults - - rusty1s - - conda-forge -dependencies: - - joblib=1.0.1 - - matplotlib=3.3.2 - - numpy=1.19.2 - - pandas=1.1.3 - - pip=20.2.4 - - scikit-learn=0.23.2 - - scipy=1.5.2 - - tqdm=4.51.0 - - pytorch=1.8.0 - - pytorch-geometric=1.7.2 - - openbabel=3.1.1 - - h5py=3.2.1 - - xtb=6.4.1 - - pip: - - ase==3.21.1 - - einops==0.3.0 - - networkx==2.5