Merge pull request deepchem#3686 from shreyasvinaya/Add-python-3.11-s…

…upport Add Python 3.11 Support
jdotsh · Mar 4, 2024 · b079607 · b079607
2 parents aaec066 + 7813c71
commit b079607
Show file tree

Hide file tree

Showing 13 changed files with 74 additions and 30 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.9']
+        python-version: ['3.9', '3.11']
     steps:
     - name: Maximize build space
       if: runner.os == 'ubuntu-latest'
@@ -78,7 +78,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.9', '3.11']
     steps:
     - uses: actions/checkout@v4
     - name: Cache pip packages for Windows

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.9', '3.11']
     steps:
     - name: Maximize build space
       if: runner.os == 'ubuntu-latest'

diff --git a/.github/workflows/jax_setup.yml b/.github/workflows/jax_setup.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
     - uses: actions/checkout@v4
     - name: Cache pip modules for Linux
@@ -39,7 +39,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     env:
       OS: ${{ matrix.os }}
       PYTHON_VERSION: ${{ matrix.python-version }}

diff --git a/.github/workflows/mini_build.yml b/.github/workflows/mini_build.yml
@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
         - os: windows-latest
           python-version: '3.9'
@@ -47,7 +47,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: 3.9
@@ -113,7 +113,7 @@ jobs:
       run: brew update && brew install libomp
     - name: Create env.yml for python >3.8
       shell: bash
-      if: ${{ matrix.python-version != '3.8' }}
+      if: ${{ matrix.python-version != '3.8' && matrix.python-version != '3.11'}}
       run: |
         python -m pip install --upgrade pip;
         pip install conda-merge;
@@ -127,6 +127,23 @@ jobs:
         fi;
         cd ..
         cp requirements/env.yml env.yml
+    - name: Create env.yml for python 3.11
+      shell: bash
+      # A special case of environment creation for python 3.8 which excludes hhsuite
+      if: ${{ matrix.python-version == '3.11' }}
+      run: |
+        python -m pip install --upgrade pip;
+        pip install conda-merge;
+        cd requirements
+        if [ "$(uname)" == 'Linux' ]; then
+          conda-merge env_common.yml env_test.yml env_ubuntu_3_11.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml
+        elif [  "$(uname)" == 'Darwin' ]; then
+          conda-merge env_common.yml env_test.yml env_mac_3_11.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml > env.yml
+        elif [[  "$(uname)" == "MINGW64_NT"* ]]; then
+          conda-merge env_common.yml env_test.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml
+        fi;
+        cd ..
+        cp requirements/env.yml env.yml
     - name: Create env.yml for python 3.8
       shell: bash
       # A special case of environment creation for python 3.8 which excludes jax [deprecated]

diff --git a/.github/workflows/tensorflow_setup.yml b/.github/workflows/tensorflow_setup.yml
@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: 3.9
@@ -43,7 +43,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: '3.9'

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: '3.9'
@@ -50,7 +50,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: '3.9'
@@ -111,17 +111,17 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Create env.yml for python 3.9
+    - name: Create env.yml for python 3.11
       shell: bash
-      if: ${{ matrix.python-version == '3.9' }}
+      if: ${{ matrix.python-version == '3.11' }}
       run: |
         python -m pip install --upgrade pip;
         pip install conda-merge;
         cd requirements
         if [ "$(uname)" == 'Linux' ]; then
-          conda-merge env_common.yml env_test.yml env_ubuntu.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml jax/env_jax.cpu.yml > env.yml
+          conda-merge env_common.yml env_test.yml env_ubuntu_3_11.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml jax/env_jax.cpu.yml >  env.yml
         elif [  "$(uname)" == 'Darwin' ]; then
-          conda-merge env_common.yml env_test.yml env_mac.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml jax/env_jax.cpu.yml > env.yml
+          conda-merge env_common.yml env_test.yml env_mac_3_11.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml jax/env_jax.cpu.yml > env.yml
         elif [[  "$(uname)" == "MINGW64_NT"* ]]; then
           conda-merge env_common.yml env_test.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml
         fi;
@@ -144,10 +144,9 @@ jobs:
         fi;
         cd ..
         cp requirements/env.yml env.yml
-    - name: Create env.yml for python == 3.10
+    - name: Create env.yml for python >= 3.9
       shell: bash
-      # A special case of environment creation for python 3.10 which excludes vina
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version != '3.8' && matrix.python-version != '3.11' }}
       run: |
         python -m pip install --upgrade pip;
         pip install conda-merge;
@@ -184,6 +183,10 @@ jobs:
       shell: bash -l {0}
       run: DGLBACKEND=pytorch pytest -v --ignore-glob='deepchem/**/test*.py' --ignore-glob='deepchem/models/jax_models/*' --doctest-modules deepchem --doctest-continue-on-failure
     - name: PyTest
-      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success')}}
+      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') && matrix.python-version == '3.11'}}
+      shell: bash -l {0}
+      run: pytest -v -m "not jax and not torch and not tensorflow and not dqc" --ignore='deepchem/utils/test/test_sequence_utils.py' deepchem
+    - name: PyTest
+      if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') && matrix.python-version != '3.11'}}
       shell: bash -l {0}
       run: pytest -v -m "not jax and not torch and not tensorflow and not dqc" deepchem
diff --git a/.github/workflows/torch_setup.yml b/.github/workflows/torch_setup.yml
@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: 3.9
@@ -43,7 +43,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.10']
+        python-version: ['3.8', '3.10', '3.11']
         include:
           - os: windows-latest
             python-version: '3.9'

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -14,7 +14,6 @@ dm-haiku
 optax
 rdkit
 torch_geometric
-git+https://github.com/diffqc/dqc.git
 PyYAML
 yamlloader
 dgl

diff --git a/requirements/env_mac_3_11.yml b/requirements/env_mac_3_11.yml
@@ -0,0 +1,8 @@
+name: deepchem
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - vina
+  - pip:
+    - pysam
diff --git a/requirements/env_ubuntu_3_11.yml b/requirements/env_ubuntu_3_11.yml
@@ -0,0 +1,8 @@
+name: deepchem
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - vina
+  - pip:
+    - pysam
diff --git a/scripts/install_deepchem_conda.ps1 b/scripts/install_deepchem_conda.ps1
@@ -20,22 +20,22 @@ conda install -c conda-forge conda-merge
 
 $common = Join-Path (pwd).PATH "requirements/env_common.yml"
 $test = Join-Path (pwd).PATH "requirements/env_test.yml"
-$tensorflow = Join-Path (pwd).PATH "requirements/tensorflow/env_tensorflow.cpu.yml"
 $out = Join-Path (pwd).PATH "env.yml"
-# Tensorflow has same installation commands for CPU and GPU
 # Torch has different installation commands for CPU and GPU
 # Jax is not supported in windows. Hence, excluded.
+# Tensorflow is not supported in windows. Hence, excluded, install 
+# linux version using Windows Subsystem for Linux.
 if($args[1] -eq "gpu")
 {
     # We expect the CUDA vesion is 10.1.
     $torch_gpu = Join-Path (pwd).PATH "requirements/torch/env_torch.gpu.yml"
-    conda-merge $common $tensorflow $torch_gpu $test > $out
+    conda-merge $common $torch_gpu $test > $out
     echo "Installing DeepChem in the GPU environment"
 }
 else
 {
     $torch_cpu = Join-Path (pwd).PATH "requirements/torch/env_torch.cpu.yml"
-    conda-merge $common $tensorflow $torch_cpu $test > $out
+    conda-merge $common $torch_cpu $test > $out
     echo "Installing DeepChem in the CPU environment"
 }
 

diff --git a/scripts/install_deepchem_conda.sh b/scripts/install_deepchem_conda.sh
@@ -28,9 +28,17 @@ then
     echo "Installing DeepChem in the GPU environment"
 else
     if [ "$(uname)" = 'Darwin' ]; then
-        conda-merge $dir/env_common.yml $dir/env_mac.yml $dir/env_test.yml $dir/tensorflow/env_tensorflow.cpu.yml $dir/torch/env_torch.mac.cpu.yml $dir/jax/env_jax.cpu.yml > $PWD/env.yml
+        if [ "$1" = "3.11" ]; then
+            conda-merge $dir/env_common.yml $dir/env_mac_3_11.yml $dir/env_test.yml $dir/tensorflow/env_tensorflow.cpu.yml $dir/torch/env_torch.mac.cpu.yml $dir/jax/env_jax.cpu.yml > $PWD/env.yml
+        else
+            conda-merge $dir/env_common.yml $dir/env_mac.yml $dir/env_test.yml $dir/tensorflow/env_tensorflow.cpu.yml $dir/torch/env_torch.mac.cpu.yml $dir/jax/env_jax.cpu.yml > $PWD/env.yml
+        fi
     elif [ "$(uname)" = 'Linux' ]; then
-        conda-merge $dir/env_common.yml $dir/env_test.yml $dir/env_ubuntu.yml $dir/tensorflow/env_tensorflow.cpu.yml $dir/torch/env_torch.cpu.yml $dir/jax/env_jax.cpu.yml > $PWD/env.yml
+        if [ "$1" = "3.11" ]; then
+            conda-merge $dir/env_common.yml $dir/env_test.yml $dir/env_ubuntu_3_11.yml $dir/tensorflow/env_tensorflow.cpu.yml $dir/torch/env_torch.cpu.yml $dir/jax/env_jax.cpu.yml > $PWD/env.yml
+        else
+            conda-merge $dir/env_common.yml $dir/env_test.yml $dir/env_ubuntu.yml $dir/tensorflow/env_tensorflow.cpu.yml $dir/torch/env_torch.cpu.yml $dir/jax/env_jax.cpu.yml > $PWD/env.yml
+        fi
     fi
     echo "Installing DeepChem in the CPU environment"
 fi

diff --git a/setup.py b/setup.py
@@ -52,6 +52,7 @@ def _get_version():
           'Programming Language :: Python :: 3.8',
           'Programming Language :: Python :: 3.9',
           'Programming Language :: Python :: 3.10',
+          'Programming Language :: Python :: 3.11',
       ],
       license='MIT',
       description='Deep learning models for drug discovery, \
@@ -79,4 +80,4 @@ def _get_version():
           'rdkit',
       ],
       extras_require=extras,
-      python_requires='>=3.7,<3.11')
+      python_requires='>=3.7,<3.12')
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,7 +14,6 @@ dm-haiku @@
     optax
     rdkit
     torch_geometric
-    git+https://github.com/diffqc/dqc.git
     PyYAML
     yamlloader
     dgl
@@ Expand Down @@