Merge pull request #6 from Exscientia/feat_sync

Sync the upstream main
OpenBioSim · May 5, 2023 · 98daa65 · 98daa65
2 parents 132c591 + 63077f0
commit 98daa65
Show file tree

Hide file tree

Showing 109 changed files with 20,591 additions and 458 deletions.
diff --git a/.github/workflows/Sandpit_exs.yml b/.github/workflows/Sandpit_exs.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.8 ambertools gromacs "sire=2023.2.2" alchemlyb pytest "openff-interchange<0.3.0"
+          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.8 ambertools gromacs "sire=2023.2.2" alchemlyb pytest "openff-interchange<0.3.0" "rdkit<2023"
           python -m pip install git+https://github.com/Exscientia/MDRestraintsGenerator.git 
           # For the testing of BSS.FreeEnergy.Relative.analysis
           python -m pip install https://github.com/alchemistry/alchemtest/archive/master.zip
@@ -49,4 +49,4 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest -v --color=yes test/Sandpit/Exscientia/
+          pytest -v --color=yes tests/Sandpit/Exscientia/
diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
@@ -0,0 +1,70 @@
+name: Release Devel
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ devel ]
+
+jobs:
+  build:
+    name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
+    runs-on: ${{ matrix.platform.os }}
+    strategy:
+      max-parallel: 9
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+        platform:
+          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
+          - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+        exclude:
+          # Exclude all but the latest Python from all but Linux
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.8"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.8"
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.9"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.9"
+    environment:
+      name: biosimspace-build
+    defaults:
+      run:
+        shell: ${{ matrix.platform.shell }}
+    env:
+      SIRE_DONT_PHONEHOME: 1
+      SIRE_SILENT_PHONEHOME: 1
+    steps:
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: bss_build
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          use-mamba: true
+#
+      - name: Clone the devel branch
+        run: git clone -b devel https://github.com/openbiosim/biosimspace
+#
+      - name: Setup Conda
+        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+#
+      - name: Update Conda recipe
+        run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
+#
+      - name: Prepare build location
+        run: mkdir ${{ github.workspace }}/build
+#
+      - name: Build Conda package using mamba build
+        run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
+#
+      - name: Upload Conda package
+        run: python ${{ github.workspace }}/biosimspace/actions/upload_package.py
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          ANACONDA_LABEL: dev
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -1,16 +1,16 @@
-name: Build
+name: Release Main
 
 on:
   workflow_dispatch:
-  push:
-    branches: [ devel ]
-  pull_request:
-    branches: [ devel ]
-
-# Note that push and pull-request builds are automatically
-# now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+    inputs:
+      upload_packages:
+        description: "Upload packages to anaconda (yes/no)?"
+        required: true
+        type: choice
+        default: 'no'
+        options:
+          - no
+          - yes
 
 jobs:
   build:
@@ -22,21 +22,9 @@ jobs:
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
         platform:
-          - {
-              name: "windows",
-              os: "windows-latest",
-              shell: "pwsh"
-            }
-          - {
-              name: "linux",
-              os: "ubuntu-latest",
-              shell: "bash -l {0}"
-            }
-          - {
-              name: "macos",
-              os: "macos-latest",
-              shell: "bash -l {0}"
-            }
+          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
+          - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
     environment:
       name: biosimspace-build
     defaults:
@@ -45,7 +33,6 @@ jobs:
     env:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
-      REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       - uses: conda-incubator/setup-miniconda@v2
         with:
@@ -56,13 +43,8 @@ jobs:
           miniforge-variant: Mambaforge
           use-mamba: true
 #
-      - name: Clone the devel branch (push to devel)
-        run: git clone https://github.com/${{ env.REPO }}
-        if: github.event_name != 'pull_request'
-#
-      - name: Clone the feature branch (pull request to devel)
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }}
-        if: github.event_name == 'pull_request'
+      - name: Clone the main branch
+        run: git clone -b main https://github.com/openbiosim/biosimspace
 #
       - name: Setup Conda
         run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
@@ -74,12 +56,11 @@ jobs:
         run: mkdir ${{ github.workspace }}/build
 #
       - name: Build Conda package using mamba build
-        run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
+        run: conda mambabuild -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
 #
       - name: Upload Conda package
         run: python ${{ github.workspace }}/biosimspace/actions/upload_package.py
         env:
-          SRC_DIR: ${{ github.workspace }}/biosimspace
-          BUILD_DIR: ${{ github.workspace }}/build
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        if: github.event_name != 'pull_request'
+          ANACONDA_LABEL: main
+        if: github.event.inputs.upload_packages == 'yes'
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -0,0 +1,70 @@
+name: Pull-Request
+
+on:
+  pull_request:
+    branches: [devel, main]
+
+jobs:
+  build:
+    name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
+    runs-on: ${{ matrix.platform.os }}
+    strategy:
+      max-parallel: 9
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+        platform:
+          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
+          - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+        exclude:
+          # Exclude all but the latest Python from all
+          # but Linux
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.8"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.8"
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.9"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.9"
+    environment:
+      name: biosimspace-build
+    defaults:
+      run:
+        shell: ${{ matrix.platform.shell }}
+    env:
+      SIRE_DONT_PHONEHOME: 1
+      SIRE_SILENT_PHONEHOME: 1
+      REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
+    steps:
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: bss_build
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          use-mamba: true
+#
+      - name: Clone the feature branch
+        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }}
+#
+      - name: Setup Conda
+        run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser
+#
+      - name: Update Conda recipe
+        run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
+#
+      - name: Prepare build location
+        run: mkdir ${{ github.workspace }}/build
+#
+      - name: Build Conda package using mamba build using main channel
+        if: ${{ github.base_ref == 'main' }}
+        run: conda mambabuild -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
+#
+      - name: Build Conda package using mamba build using dev channel
+        if: ${{ github.base_ref != 'main' }}
+        run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
diff --git a/RELEASE_INSTRUCTIONS.rst b/RELEASE_INSTRUCTIONS.rst
@@ -1,66 +1,4 @@
 BioSimSpace release instructions
 *********************************
 
-The following instructions describe how to create a new BioSimSpace release:
-
-Step 1
-======
-
-Update the `CHANGELOG <https://github.com/openbiosim/biosimspace/blob/devel/doc/source/changelog.rst>`_
-file with a summary of the changes for this relase. Feel free to link to
-`GitHub issues <https://github.com/openbiosim/biosimspace/issues>`_ where relevant
-and give credit for specific contributions.
-
-Step 2
-======
-
-When you're happy, tag the commit that you want to be associated with the
-release. The following will tag the latest commit:
-
-.. code-block:: bash
-
-    git tag -a 2023.1.0 -m "Tagging the 2023.1.0 release of BioSimSpace."
-
-Step 3
-======
-
-Push the commit and tag to the ``devel`` branch on the remote:
-
-.. code-block:: bash
-
-    git push origin devel --follow-tags
-
-This will trigger a new Azure Pipelines build which will create binaries
-and Conda packages for the release. If you make a mistake and want to move
-the tag to a later commit, simply delete the tag from the remote:
-
-.. code-block:: bash
-
-    git push origin :refs/tags/2023.1.0
-
-Next, delete the Conda release package from the `Anaconda Cloud <https://anaconda.org/openbiosim/biosimspace/files>`_.
-You can then move the tag to the latest commit:
-
-.. code-block:: bash
-
-    git tag -fa 2023.1.0
-
-Finally, push the new commit and updated tag:
-
-.. code-block:: bash
-
-    git push origin devel --follow-tags
-
-Step 4
-======
-
-Create a `GitHub release <https://github.com/openbiosim/biosimspace/releases>`_.
-When drafting the release, simply choose the tag that you have created.
-
-Step 5
-======
-
-Create a `pull request <https://github.com/openbiosim/biosimspace/pulls>`_ to
-merge ``devel`` into the ``master`` branch.
-
-That's it!
+Please see the instructions on our website `here <https://biosimspace.openbiosim.org/contributing/packaging.html#creating-releases>`__
diff --git a/actions/upload_package.py b/actions/upload_package.py
@@ -16,6 +16,12 @@
 else:
     conda_token = "TEST"
 
+# Get the anaconda channel labels.
+if "ANACONDA_LABEL" in os.environ:
+    conda_label = os.environ["ANACONDA_LABEL"]
+else:
+    conda_label = "dev"
+
 # get the root conda directory
 conda = os.environ["CONDA"]
 
@@ -50,17 +56,8 @@ def run_cmd(cmd):
 
 tag = run_cmd(f"git --git-dir={gitdir} --work-tree={srcdir} tag --contains")
 
-# If the tag is not empty, then set the label to main (this is a release)
-if tag is not None and tag.lstrip().rstrip() != "":
-    print(f"\nTag {tag} is set. This is a 'main' release.")
-    label = "--label main --label dev"
-else:
-    # this is a development release
-    print("\nNo tag is set. This is a 'devel' release.")
-    label = "--label dev"
-
 # Upload the packages to the openbiosim channel on Anaconda Cloud.
-cmd = f"anaconda --token {conda_token} upload --user openbiosim {label} --force {packages}"
+cmd = f"anaconda --token {conda_token} upload --user openbiosim --label {conda_label} --force {packages}"
 
 print(f"\nUpload command:\n\n{cmd}\n")
 

diff --git a/doc/source/api/index_Convert.rst b/doc/source/api/index_Convert.rst
@@ -1,4 +1,4 @@
-.. _ref-Box:
+.. _ref-Convert:
 
 BioSimSpace.Convert
 ===================

diff --git a/doc/source/contributing/development.rst b/doc/source/contributing/development.rst
@@ -205,25 +205,25 @@ To run the full test suite, simply type:
 
 .. code-block:: bash
 
-   pytest
+   pytest tests
 
 To run tests for a specific sub-module, e.g.:
 
 .. code-block:: bash
 
-   pytest test/Process
+   pytest tests/Process
 
 To only run the unit tests in a particular file, e.g.:
 
 .. code-block:: bash
 
-   pytest test/Process/test_namd.py
+   pytest tests/Process/test_namd.py
 
 To run a specific unit tests in a particular file, e.g.:
 
 .. code-block:: bash
 
-   pytest test/Process/test_namd.py::test_minimise
+   pytest tests/Process/test_namd.py::test_minimise
 
 To get more detailed information about each test, run pytests using the
 *verbose* flag, e.g.: