From 47ab592d9069ddf3cf1a2339d11f8138be48573c Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Thu, 20 Jun 2024 16:33:07 +0200 Subject: [PATCH 01/16] add ranges for pip dependenciesw --- pyproject.toml | 52 +++++++++++++++++++++++++------------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6c95ec6c..336f82c0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,38 +35,38 @@ classifiers = [ "Programming Language :: Python :: 3.10", ] dependencies = [ - "notebook >= 7.0.6", - "markov-clustering >= 0.0.6.dev0", - "tensorboard>=0.9.0", - "protobuf >= 3.20.1", - "dill >= 0.3.8", - "pyarrow >= 15.0.0", - "tables >= 3.8.0", + "notebook >= 7.0.6, < 8.0", + "markov-clustering >= 0.0.6.dev0, < 1.0", + "tensorboard>=0.9.0, < 1.0", + "protobuf >= 3.20.1, < 4.0", + "dill >= 0.3.8, < 1.0", + "pyarrow >= 15.0.0, < 16.0", + "tables >= 3.8.0, < 4.0", "numpy >= 1.25, < 2.0", - "scipy >= 1.13.1", - "h5py >= 3.6.0", - "networkx >= 2.6.3", - "matplotlib >= 3.5.1", - "scikit-learn >= 1.0.2", - "chart-studio >= 1.1.0", - "pdb2sql >= 0.5.1", - "python-louvain >= 0.16", - "tqdm >= 4.63.0", - "freesasa >= 2.1.0", - "biopython >= 1.81" + "scipy >= 1.13.1, < 2.0", + "h5py >= 3.6.0, < 4.0", + "networkx >= 2.6.3, < 3.0", + "matplotlib >= 3.5.1, < 4.0", + "scikit-learn >= 1.0.2, < 2.0", + "chart-studio >= 1.1.0, < 2.0", + "pdb2sql >= 0.5.1, < 1.0", + "python-louvain >= 0.16, < 1.0", + "tqdm >= 4.63.0, < 5.0", + "freesasa >= 2.1.0, < 3.0", + "biopython >= 1.81, < 2.0" ] [project.optional-dependencies] # development dependency groups test = [ - "pytest >= 7.4.0", - "bump2version", - "coverage", - "pycodestyle", - "pytest-cov", - "pytest-runner", - "coveralls", - "ruff>=0.3.0" + "pytest >= 7.4.0, < 8.0", + "bump2version >= 1.0.1, < 2.0", + "coverage >= 6.5.0, < 7.0", + "pycodestyle >= 2.8.0, < 3.0", + "pytest-cov >= 4.1.0, < 5.0", + "pytest-runner >= 6.0.0, < 7.0", + "coveralls >= 3.3.1, < 4.0", + "ruff >= 0.3.0, < 1.0" ] publishing = ["build", "twine", "wheel"] notebooks = ["nbmake"] From fc3782ab9363514efaa6fe704d1ac25a1bdd4d8c Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Thu, 20 Jun 2024 16:41:16 +0200 Subject: [PATCH 02/16] fix tensorboard version range --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 336f82c0..5c156d4a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ classifiers = [ dependencies = [ "notebook >= 7.0.6, < 8.0", "markov-clustering >= 0.0.6.dev0, < 1.0", - "tensorboard>=0.9.0, < 1.0", + "tensorboard >= 1.0.0, < 2.0", "protobuf >= 3.20.1, < 4.0", "dill >= 0.3.8, < 1.0", "pyarrow >= 15.0.0, < 16.0", From 3104a31c2bccef93242d145f6b0a5fd174f36cf5 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Thu, 20 Jun 2024 17:24:11 +0200 Subject: [PATCH 03/16] degrade numpy range --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5c156d4a..dbd22d32 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,7 @@ dependencies = [ "dill >= 0.3.8, < 1.0", "pyarrow >= 15.0.0, < 16.0", "tables >= 3.8.0, < 4.0", - "numpy >= 1.25, < 2.0", + "numpy >= 1.20, < 1.24", "scipy >= 1.13.1, < 2.0", "h5py >= 3.6.0, < 4.0", "networkx >= 2.6.3, < 3.0", From f458d171048c773551fde50a8a226c9110654874 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Thu, 20 Jun 2024 17:29:32 +0200 Subject: [PATCH 04/16] update min versions pip --- pyproject.toml | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index dbd22d32..9e8be130 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,25 +35,25 @@ classifiers = [ "Programming Language :: Python :: 3.10", ] dependencies = [ - "notebook >= 7.0.6, < 8.0", + "notebook >= 7.2.1, < 8.0", "markov-clustering >= 0.0.6.dev0, < 1.0", - "tensorboard >= 1.0.0, < 2.0", - "protobuf >= 3.20.1, < 4.0", + "tensorboard >= 2.17.0, < 3.0", + "protobuf >= 5.27.1, < 6.0", "dill >= 0.3.8, < 1.0", - "pyarrow >= 15.0.0, < 16.0", - "tables >= 3.8.0, < 4.0", - "numpy >= 1.20, < 1.24", + "pyarrow >= 16.1.0, < 17.0", + "tables >= 3.9.2, < 4.0", + "numpy >= 1.25, < 2.0", "scipy >= 1.13.1, < 2.0", - "h5py >= 3.6.0, < 4.0", - "networkx >= 2.6.3, < 3.0", - "matplotlib >= 3.5.1, < 4.0", - "scikit-learn >= 1.0.2, < 2.0", + "h5py >= 3.11.0, < 4.0", + "networkx >= 3.3.3, < 4.0", + "matplotlib >= 3.9.0, < 4.0", + "scikit-learn >= 1.5.0, < 2.0", "chart-studio >= 1.1.0, < 2.0", - "pdb2sql >= 0.5.1, < 1.0", + "pdb2sql >= 0.5.3, < 1.0", "python-louvain >= 0.16, < 1.0", - "tqdm >= 4.63.0, < 5.0", - "freesasa >= 2.1.0, < 3.0", - "biopython >= 1.81, < 2.0" + "tqdm >= 4.66.4, < 5.0", + "freesasa >= 2.1.1, < 3.0", + "biopython >= 1.83, < 2.0" ] [project.optional-dependencies] From 49bf53c1f552debb4268411f44d5c31f75a1c203 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Fri, 21 Jun 2024 10:33:11 +0200 Subject: [PATCH 05/16] fix networkx lower bound version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9e8be130..14a0c4d1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ dependencies = [ "numpy >= 1.25, < 2.0", "scipy >= 1.13.1, < 2.0", "h5py >= 3.11.0, < 4.0", - "networkx >= 3.3.3, < 4.0", + "networkx >= 3.1, < 4.0", "matplotlib >= 3.9.0, < 4.0", "scikit-learn >= 1.5.0, < 2.0", "chart-studio >= 1.1.0, < 2.0", From f6260bcaa1b002f36bc6b2ab2188240ab8b8365c Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Fri, 21 Jun 2024 10:39:04 +0200 Subject: [PATCH 06/16] change lower bound protobuf to solve conflict --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 14a0c4d1..8d234757 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ dependencies = [ "notebook >= 7.2.1, < 8.0", "markov-clustering >= 0.0.6.dev0, < 1.0", "tensorboard >= 2.17.0, < 3.0", - "protobuf >= 5.27.1, < 6.0", + "protobuf >= 5.24.3, < 6.0", "dill >= 0.3.8, < 1.0", "pyarrow >= 16.1.0, < 17.0", "tables >= 3.9.2, < 4.0", From 5befe6250d88b00024345aecc7c5068592bd3a9a Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Fri, 21 Jun 2024 10:50:22 +0200 Subject: [PATCH 07/16] edit lower bounds versions --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8d234757..b735f143 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,8 +37,8 @@ classifiers = [ dependencies = [ "notebook >= 7.2.1, < 8.0", "markov-clustering >= 0.0.6.dev0, < 1.0", - "tensorboard >= 2.17.0, < 3.0", - "protobuf >= 5.24.3, < 6.0", + "tensorboard >= 0.9.0, < 3.0", + "protobuf >= 3.20.1, < 6.0", "dill >= 0.3.8, < 1.0", "pyarrow >= 16.1.0, < 17.0", "tables >= 3.9.2, < 4.0", From f5a9e772d3846beb92f414bf38e8bf740d032e3b Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Fri, 21 Jun 2024 12:02:04 +0200 Subject: [PATCH 08/16] fix conda critical deps --- env/deeprank2.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/env/deeprank2.yml b/env/deeprank2.yml index 423fab5c..f80243ef 100644 --- a/env/deeprank2.yml +++ b/env/deeprank2.yml @@ -7,14 +7,14 @@ channels: - conda-forge - sbl dependencies: - - sbl::libcifpp>=5.1.0 - - sbl::dssp>=4.2.2.1 - - msms>=2.6.1 + - sbl::libcifpp=5.1.0 + - sbl::dssp=4.2.2.1 + - msms=2.6.1 - pytorch=2.1.1 - torchvision>=0.16.1 - torchaudio>=2.1.1 - cpuonly>=2.0 - - pyg>=2.4.0 + - pyg=2.4.0 - pytorch-scatter>=2.1.2 - pytorch-sparse>=0.6.18 - pytorch-cluster>=1.6.3 From 99fc5e0a53493a4243d496897fa432d0928e18a2 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Fri, 21 Jun 2024 15:43:28 +0200 Subject: [PATCH 09/16] add python version spec --- env/deeprank2.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/env/deeprank2.yml b/env/deeprank2.yml index f80243ef..4e5d7b64 100644 --- a/env/deeprank2.yml +++ b/env/deeprank2.yml @@ -7,6 +7,8 @@ channels: - conda-forge - sbl dependencies: + - python=3.10 + - pip>=23.3 - sbl::libcifpp=5.1.0 - sbl::dssp=4.2.2.1 - msms=2.6.1 From fc4662cc3d83eda9547f30e79963db89d4a3e447 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 10:26:40 +0200 Subject: [PATCH 10/16] fix ruff version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b735f143..f697d526 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ test = [ "pytest-cov >= 4.1.0, < 5.0", "pytest-runner >= 6.0.0, < 7.0", "coveralls >= 3.3.1, < 4.0", - "ruff >= 0.3.0, < 1.0" + "ruff == 0.5.1" ] publishing = ["build", "twine", "wheel"] notebooks = ["nbmake"] From d971eb501a0fa1c006862a685a39d7783b28b354 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 10:27:57 +0200 Subject: [PATCH 11/16] add freezed env and test it on the ci --- .../install-python-and-package/action.yml | 15 +- .github/workflows/build-repo-freezed-env.yml | 60 +++++ env/deeprank2_freezed.yml | 234 ++++++++++++++++++ 3 files changed, 308 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/build-repo-freezed-env.yml create mode 100644 env/deeprank2_freezed.yml diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml index 9f725336..a5884bcb 100644 --- a/.github/actions/install-python-and-package/action.yml +++ b/.github/actions/install-python-and-package/action.yml @@ -39,6 +39,19 @@ runs: activate-environment: deeprank2 environment-file: env/deeprank2.yml use-mamba: true + if: ${{ inputs.pkg-installation-type != 'freezed' }} + + - name: Setup miniconda with freezed dependencies + uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + miniforge-variant: Mambaforge + channels: conda-forge + python-version: ${{ inputs.python-version }} + activate-environment: deeprank2 + environment-file: env/deeprank2_freezed.yml + use-mamba: true + if: ${{ inputs.pkg-installation-type == 'freezed' }} - run: | conda --version @@ -53,7 +66,7 @@ runs: - name: Install the GitHub repository version of the package shell: bash -l {0} - if: ${{ inputs.pkg-installation-type == 'repository' }} + if: ${{ inputs.pkg-installation-type == 'repository' || inputs.pkg-installation-type == 'freezed' }} run: | conda activate deeprank2 pip install .'[${{ inputs.extras-require }}]' diff --git a/.github/workflows/build-repo-freezed-env.yml b/.github/workflows/build-repo-freezed-env.yml new file mode 100644 index 00000000..9a009d15 --- /dev/null +++ b/.github/workflows/build-repo-freezed-env.yml @@ -0,0 +1,60 @@ +name: build (repository package) using the freezed environment + +on: + push: + paths-ignore: + # specific folder locations + - ".vscode/**" + - "docs/**" + # filetypes + - "**.md" + - "**.rst" + - "**.ipynb" + - "**.cff" + - "**.png" + branches: + - main + pull_request: + types: [opened, synchronize, reopened, ready_for_review] + paths-ignore: + # specific folder locations + - ".vscode/**" + - "docs/**" + # filetypes + - "**.md" + - "**.rst" + - "**.ipynb" + - "**.cff" + - "**.png" + +jobs: + build: + if: github.event.pull_request.draft == false + name: Build for (${{ matrix.python-version }}, ${{ matrix.os }}) + runs-on: ${{ matrix.os }} + + strategy: + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.10"] # ["3.10", "3.11"] + + # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell + defaults: + run: + shell: bash -l {0} + + steps: + - uses: actions/checkout@v3 + + - uses: ./.github/actions/install-python-and-package + with: + python-version: ${{ matrix.python-version }} + extras-require: test, publishing + pkg-installation-type: "freezed" + + - name: Run unit tests + run: pytest -v + + - name: Verify that we can build the package + run: python3 -m build diff --git a/env/deeprank2_freezed.yml b/env/deeprank2_freezed.yml new file mode 100644 index 00000000..bab6c797 --- /dev/null +++ b/env/deeprank2_freezed.yml @@ -0,0 +1,234 @@ +name: deeprank2 +channels: + - pyg + - bioconda + - sbl + - pytorch + - defaults + - conda-forge +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - blas=1.0=mkl + - brotli-python=1.0.9=py310h6a678d5_8 + - bzip2=1.0.8=h5eee18b_6 + - ca-certificates=2024.3.11=h06a4308_0 + - certifi=2024.6.2=py310h06a4308_0 + - charset-normalizer=2.0.4=pyhd3eb1b0_0 + - cpuonly=2.0=0 + - dssp=4.2.2.1=h3fd9d12_0 + - ffmpeg=4.3=hf484d3e_0 + - filelock=3.13.1=py310h06a4308_0 + - freetype=2.12.1=h4a9f257_0 + - gmp=6.2.1=h295c915_3 + - gmpy2=2.1.2=py310heeb90bb_0 + - gnutls=3.6.15=he1e5248_0 + - idna=3.7=py310h06a4308_0 + - intel-openmp=2023.1.0=hdb19cb5_46306 + - jinja2=3.1.4=py310h06a4308_0 + - joblib=1.4.2=py310h06a4308_0 + - jpeg=9e=h5eee18b_1 + - lame=3.100=h7b6447c_0 + - lcms2=2.12=h3be6417_0 + - ld_impl_linux-64=2.38=h1181459_1 + - lerc=3.0=h295c915_0 + - libcifpp=5.1.0=hf65b397_0 + - libdeflate=1.17=h5eee18b_1 + - libffi=3.4.4=h6a678d5_1 + - libgcc-ng=13.2.0=h77fa898_11 + - libgfortran-ng=11.2.0=h00389a5_1 + - libgfortran5=11.2.0=h1234567_1 + - libgomp=13.2.0=h77fa898_11 + - libiconv=1.16=h5eee18b_3 + - libidn2=2.3.4=h5eee18b_0 + - libjpeg-turbo=2.0.0=h9bf148f_0 + - libmcfp=1.2.3=h3fd9d12_0 + - libpng=1.6.39=h5eee18b_0 + - libstdcxx-ng=13.2.0=hc0a3c3a_11 + - libtasn1=4.19.0=h5eee18b_0 + - libtiff=4.5.1=h6a678d5_0 + - libunistring=0.9.10=h27cfd23_0 + - libuuid=1.41.5=h5eee18b_0 + - libwebp-base=1.3.2=h5eee18b_0 + - libzlib=1.2.13=h4ab18f5_6 + - llvm-openmp=14.0.6=h9e868ea_0 + - lz4-c=1.9.4=h6a678d5_1 + - markupsafe=2.1.3=py310h5eee18b_0 + - mkl=2023.1.0=h213fc3f_46344 + - mkl-service=2.4.0=py310h5eee18b_1 + - mkl_fft=1.3.8=py310h5eee18b_0 + - mkl_random=1.2.4=py310hdb19cb5_0 + - mpc=1.1.0=h10f8cd9_1 + - mpfr=4.0.2=hb69a4c5_1 + - mpmath=1.3.0=py310h06a4308_0 + - msms=2.6.1=h9ee0642_3 + - ncurses=6.4=h6a678d5_0 + - nettle=3.7.3=hbbd107a_1 + - networkx=3.2.1=py310h06a4308_0 + - numpy=1.26.4=py310h5f9d8c6_0 + - numpy-base=1.26.4=py310hb5e798b_0 + - openh264=2.1.1=h4ff587b_0 + - openjpeg=2.4.0=h3ad879b_0 + - openssl=3.0.14=h5eee18b_0 + - pillow=10.3.0=py310h5eee18b_0 + - pip=24.0=py310h06a4308_0 + - psutil=5.9.0=py310h5eee18b_0 + - pybind11-abi=4=hd3eb1b0_1 + - pyg=2.4.0=py310_torch_2.1.0_cpu + - pyparsing=3.0.9=py310h06a4308_0 + - pysocks=1.7.1=py310h06a4308_0 + - python=3.10.14=h955ad1f_1 + - pytorch=2.1.1=py3.10_cpu_0 + - pytorch-cluster=1.6.3=py310_torch_2.1.0_cpu + - pytorch-mutex=1.0=cpu + - pytorch-scatter=2.1.2=py310_torch_2.1.0_cpu + - pytorch-sparse=0.6.18=py310_torch_2.1.0_cpu + - pytorch-spline-conv=1.2.2=py310_torch_2.1.0_cpu + - pyyaml=6.0.1=py310h5eee18b_0 + - readline=8.2=h5eee18b_0 + - requests=2.32.2=py310h06a4308_0 + - scipy=1.13.1=py310h5f9d8c6_0 + - setuptools=69.5.1=py310h06a4308_0 + - sqlite=3.45.3=h5eee18b_0 + - sympy=1.12=py310h06a4308_0 + - tbb=2021.8.0=hdb19cb5_0 + - tk=8.6.14=h39e8969_0 + - torchaudio=2.1.1=py310_cpu + - torchvision=0.16.1=py310_cpu + - tqdm=4.66.4=py310h2f386ee_0 + - typing_extensions=4.11.0=py310h06a4308_0 + - urllib3=2.2.2=py310h06a4308_0 + - wheel=0.43.0=py310h06a4308_0 + - xz=5.4.6=h5eee18b_1 + - yaml=0.2.5=h7b6447c_0 + - zlib=1.2.13=h4ab18f5_6 + - zstd=1.5.5=hc292b87_2 + - pip: + - absl-py==2.1.0 + - anyio==4.4.0 + - argon2-cffi==23.1.0 + - argon2-cffi-bindings==21.2.0 + - arrow==1.3.0 + - asttokens==2.4.1 + - async-lru==2.0.4 + - attrs==23.2.0 + - babel==2.15.0 + - beautifulsoup4==4.12.3 + - biopython==1.83 + - bleach==6.1.0 + - blosc2==2.7.0 + - bump2version==1.0.1 + - cffi==1.16.0 + - chart-studio==1.1.0 + - comm==0.2.2 + - contourpy==1.2.1 + - coverage==6.5.0 + - coveralls==3.3.1 + - cycler==0.12.1 + - debugpy==1.8.1 + - decorator==5.1.1 + - defusedxml==0.7.1 + - dill==0.3.8 + - docopt==0.6.2 + - exceptiongroup==1.2.1 + - executing==2.0.1 + - fastjsonschema==2.20.0 + - fonttools==4.53.0 + - fqdn==1.5.1 + - freesasa==2.2.1 + - grpcio==1.64.1 + - h11==0.14.0 + - h5py==3.11.0 + - httpcore==1.0.5 + - httpx==0.27.0 + - iniconfig==2.0.0 + - ipykernel==6.29.4 + - ipython==8.25.0 + - isoduration==20.11.0 + - jedi==0.19.1 + - json5==0.9.25 + - jsonpointer==3.0.0 + - jsonschema==4.22.0 + - jsonschema-specifications==2023.12.1 + - jupyter-client==8.6.2 + - jupyter-core==5.7.2 + - jupyter-events==0.10.0 + - jupyter-lsp==2.2.5 + - jupyter-server==2.14.1 + - jupyter-server-terminals==0.5.3 + - jupyterlab==4.2.2 + - jupyterlab-pygments==0.3.0 + - jupyterlab-server==2.27.2 + - kiwisolver==1.4.5 + - markdown==3.6 + - markov-clustering==0.0.6.dev0 + - matplotlib==3.9.0 + - matplotlib-inline==0.1.7 + - mistune==3.0.2 + - msgpack==1.0.8 + - nbclient==0.10.0 + - nbconvert==7.16.4 + - nbformat==5.10.4 + - ndindex==1.8 + - nest-asyncio==1.6.0 + - notebook==7.2.1 + - notebook-shim==0.2.4 + - numexpr==2.10.1 + - overrides==7.7.0 + - packaging==24.1 + - pandas==2.2.2 + - pandocfilters==1.5.1 + - parso==0.8.4 + - pdb2sql==0.5.3 + - pexpect==4.9.0 + - platformdirs==4.2.2 + - plotly==5.22.0 + - pluggy==1.5.0 + - prometheus-client==0.20.0 + - prompt-toolkit==3.0.47 + - protobuf==4.25.3 + - ptyprocess==0.7.0 + - pure-eval==0.2.2 + - py-cpuinfo==9.0.0 + - pyarrow==16.1.0 + - pycodestyle==2.12.0 + - pycparser==2.22 + - pygments==2.18.0 + - pytest==7.4.4 + - pytest-cov==4.1.0 + - pytest-runner==6.0.1 + - python-dateutil==2.9.0.post0 + - python-json-logger==2.0.7 + - python-louvain==0.16 + - pytz==2024.1 + - pyzmq==26.0.3 + - referencing==0.35.1 + - retrying==1.3.4 + - rfc3339-validator==0.1.4 + - rfc3986-validator==0.1.1 + - rpds-py==0.18.1 + - ruff==0.4.10 + - scikit-learn==1.5.0 + - send2trash==1.8.3 + - six==1.16.0 + - sniffio==1.3.1 + - soupsieve==2.5 + - stack-data==0.6.3 + - tables==3.9.2 + - tenacity==8.4.1 + - tensorboard==2.17.0 + - tensorboard-data-server==0.7.2 + - terminado==0.18.1 + - threadpoolctl==3.5.0 + - tinycss2==1.3.0 + - tomli==2.0.1 + - tornado==6.4.1 + - traitlets==5.14.3 + - types-python-dateutil==2.9.0.20240316 + - tzdata==2024.1 + - uri-template==1.3.0 + - wcwidth==0.2.13 + - webcolors==24.6.0 + - webencodings==0.5.1 + - websocket-client==1.8.0 + - werkzeug==3.0.3 From 655e839acde8b76da359fc33dfc32f793f207ad0 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 10:46:02 +0200 Subject: [PATCH 12/16] add ref to freezed env --- README.md | 2 ++ docs/installation.md | 8 +++++--- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4482c0d7..375815c7 100644 --- a/README.md +++ b/README.md @@ -121,6 +121,8 @@ conda activate deeprank2 pip install deeprank2 ``` +We also provide a frozen environment YML file located at `env/deeprank2_freezed.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. + See instructions below to [test](#testing-deeprank2-installation) that the installation was succesful. #### Manual installation (customizable) diff --git a/docs/installation.md b/docs/installation.md index 394a28d0..831a3976 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -4,9 +4,9 @@ - [Installation](#installation) - [Containerized Installation](#containerized-installation) - [Local/remote installation](#localremote-installation) - - [YML file installation (recommended)](#yml-file-installation-recommended) - - [Manual installation (customizable)](#manual-installation-customizable) - - [Testing DeepRank2 installation](#testing-deeprank2-installation) + - [YML file installation (recommended)](#yml-file-installation-recommended) + - [Manual installation (customizable)](#manual-installation-customizable) + - [Testing DeepRank2 installation](#testing-deeprank2-installation) - [Contributing](#contributing) # Installation @@ -67,6 +67,8 @@ conda activate deeprank2 pip install deeprank2 ``` +We also provide a frozen environment YML file located at `env/deeprank2_freezed.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. + See instructions below to [test](#testing-deeprank2-installation) that the installation was succesful. #### Manual installation (customizable) From 252ebe48184d948322572d947b86ab719c1ea18a Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 11:19:34 +0200 Subject: [PATCH 13/16] change freezed to frozen --- .github/actions/install-python-and-package/action.yml | 10 +++++----- .github/workflows/build-repo-freezed-env.yml | 4 ++-- README.md | 2 +- docs/installation.md | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/actions/install-python-and-package/action.yml b/.github/actions/install-python-and-package/action.yml index a5884bcb..539cfe42 100644 --- a/.github/actions/install-python-and-package/action.yml +++ b/.github/actions/install-python-and-package/action.yml @@ -39,9 +39,9 @@ runs: activate-environment: deeprank2 environment-file: env/deeprank2.yml use-mamba: true - if: ${{ inputs.pkg-installation-type != 'freezed' }} + if: ${{ inputs.pkg-installation-type != 'frozen' }} - - name: Setup miniconda with freezed dependencies + - name: Setup miniconda with frozen dependencies uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true @@ -49,9 +49,9 @@ runs: channels: conda-forge python-version: ${{ inputs.python-version }} activate-environment: deeprank2 - environment-file: env/deeprank2_freezed.yml + environment-file: env/deeprank2_frozen.yml use-mamba: true - if: ${{ inputs.pkg-installation-type == 'freezed' }} + if: ${{ inputs.pkg-installation-type == 'frozen' }} - run: | conda --version @@ -66,7 +66,7 @@ runs: - name: Install the GitHub repository version of the package shell: bash -l {0} - if: ${{ inputs.pkg-installation-type == 'repository' || inputs.pkg-installation-type == 'freezed' }} + if: ${{ inputs.pkg-installation-type == 'repository' || inputs.pkg-installation-type == 'frozen' }} run: | conda activate deeprank2 pip install .'[${{ inputs.extras-require }}]' diff --git a/.github/workflows/build-repo-freezed-env.yml b/.github/workflows/build-repo-freezed-env.yml index 9a009d15..47f29dce 100644 --- a/.github/workflows/build-repo-freezed-env.yml +++ b/.github/workflows/build-repo-freezed-env.yml @@ -1,4 +1,4 @@ -name: build (repository package) using the freezed environment +name: build (repository package) using the frozen environment on: push: @@ -51,7 +51,7 @@ jobs: with: python-version: ${{ matrix.python-version }} extras-require: test, publishing - pkg-installation-type: "freezed" + pkg-installation-type: "frozen" - name: Run unit tests run: pytest -v diff --git a/README.md b/README.md index 375815c7..09f6fd08 100644 --- a/README.md +++ b/README.md @@ -121,7 +121,7 @@ conda activate deeprank2 pip install deeprank2 ``` -We also provide a frozen environment YML file located at `env/deeprank2_freezed.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. +We also provide a frozen environment YML file located at `env/deeprank2_frozen.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. See instructions below to [test](#testing-deeprank2-installation) that the installation was succesful. diff --git a/docs/installation.md b/docs/installation.md index 831a3976..ced3f9b3 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -67,7 +67,7 @@ conda activate deeprank2 pip install deeprank2 ``` -We also provide a frozen environment YML file located at `env/deeprank2_freezed.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. +We also provide a frozen environment YML file located at `env/deeprank2_frozen.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. See instructions below to [test](#testing-deeprank2-installation) that the installation was succesful. From 107e52cb4cac5cc126cfa96ea34af3f5a8c0069b Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 11:23:59 +0200 Subject: [PATCH 14/16] add comment about when to use the frozen env --- README.md | 2 +- docs/installation.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 0ce08569..f7fa6c36 100644 --- a/README.md +++ b/README.md @@ -115,7 +115,7 @@ conda activate deeprank2 pip install deeprank2 ``` -We also provide a frozen environment YML file located at `env/deeprank2_frozen.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. +We also provide a frozen environment YML file located at `env/deeprank2_frozen.yml` with all dependencies set to fixed versions. The `env/deeprank2_frozen.yml` file provides a frozen environment with all dependencies set to fixed versions. This ensures reproducibility of experiments and results by preventing changes in package versions that could occur due to updates or modifications in the default `env/deeprank2.yml`. Use this frozen environment file for a stable and consistent setup, particularly if you encounter issues with the default environment file. #### Manual installation (customizable) diff --git a/docs/installation.md b/docs/installation.md index 091894b2..05cfb6a4 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -61,7 +61,7 @@ conda activate deeprank2 pip install deeprank2 ``` -We also provide a frozen environment YML file located at `env/deeprank2_frozen.yml` with all dependencies set to fixed versions. If necessary, this file can be used instead of `env/deeprank2.yml`. +We also provide a frozen environment YML file located at `env/deeprank2_frozen.yml` with all dependencies set to fixed versions. The `env/deeprank2_frozen.yml` file provides a frozen environment with all dependencies set to fixed versions. This ensures reproducibility of experiments and results by preventing changes in package versions that could occur due to updates or modifications in the default `env/deeprank2.yml`. Use this frozen environment file for a stable and consistent setup, particularly if you encounter issues with the default environment file. #### Manual installation (customizable) From 79b5331716e763e25348c7954738a3c74248bd84 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 11:26:21 +0200 Subject: [PATCH 15/16] rename frozen env file --- env/{deeprank2_freezed.yml => deeprank2_frozen.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename env/{deeprank2_freezed.yml => deeprank2_frozen.yml} (100%) diff --git a/env/deeprank2_freezed.yml b/env/deeprank2_frozen.yml similarity index 100% rename from env/deeprank2_freezed.yml rename to env/deeprank2_frozen.yml From 602354f0b1f4dc6100af20784cfe4b983b748d67 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Tue, 9 Jul 2024 11:31:47 +0200 Subject: [PATCH 16/16] rename to frozen --- .../{build-repo-freezed-env.yml => build-repo-frozen-env.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{build-repo-freezed-env.yml => build-repo-frozen-env.yml} (100%) diff --git a/.github/workflows/build-repo-freezed-env.yml b/.github/workflows/build-repo-frozen-env.yml similarity index 100% rename from .github/workflows/build-repo-freezed-env.yml rename to .github/workflows/build-repo-frozen-env.yml