Merge pull request #35 from OpenBioSim/fix_ci

Update CI for new release process on main
OpenBioSim · Apr 14, 2023 · 083dc3e · 083dc3e
2 parents df133ed + 52d8d0c
commit 083dc3e
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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
@@ -1,17 +1,12 @@
-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
+        default: "no"
 jobs:
   build:
     name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
@@ -22,21 +17,9 @@ jobs:
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
         platform:
-          - {
-              name: "windows",
-              os: "windows-latest",
-              shell: "pwsh"
-            }
-          - {
-              name: "linux",
-              os: "ubuntu-latest",
-              shell: "bash -l {0}"
-            }
-          - {
-              name: "macos",
-              os: "macos-latest",
-              shell: "bash -l {0}"
-            }
+          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
+          - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
     environment:
       name: biosimspace-build
     defaults:
@@ -45,7 +28,6 @@ jobs:
     env:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
-      REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       - uses: conda-incubator/setup-miniconda@v2
         with:
@@ -56,13 +38,8 @@ 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 +51,11 @@ 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/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/python/BioSimSpace/IO/_io.py b/python/BioSimSpace/IO/_io.py
@@ -420,6 +420,9 @@ def readMolecules(files, show_warnings=False, download_dir=None, property_map={}
             raise TypeError("'files' must be a list of 'str' types.")
         if len(files) == 0:
             raise ValueError("The list of input files is empty!")
+        # Convert tuple to list.
+        if isinstance(files, tuple):
+            files = list(files)
     else:
         raise TypeError("'files' must be of type 'str', or a list of 'str' types.")
 

diff --git a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
@@ -420,6 +420,9 @@ def readMolecules(files, show_warnings=False, download_dir=None, property_map={}
             raise TypeError("'files' must be a list of 'str' types.")
         if len(files) == 0:
             raise ValueError("The list of input files is empty!")
+        # Convert tuple to list.
+        if isinstance(files, tuple):
+            files = list(files)
     else:
         raise TypeError("'files' must be of type 'str', or a list of 'str' types.")
 

diff --git a/python/setup.py b/python/setup.py
@@ -39,7 +39,7 @@
         )
 
     # Check the Sire version.
-    if int(sire.legacy.__version__.replace(".", "")) < min_ver_int:
+    if int(sire.legacy.__version__.replace(".", "").replace("dev", "")) < min_ver_int:
         raise ImportError("BioSimSpace requires Sire version '%s' or above." % min_ver)
 
 from setuptools import setup, find_packages

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,10 @@
 # BioSimSpace runtime requirements.
 
-sire ~=2023.2.0
+# main
+sire~=2023.2.2
+
+# devel
+#sire==2023.3.0.dev
 
 configargparse
 ipywidgets<8

diff --git a/test/IO/test_tuple.py b/test/IO/test_tuple.py
@@ -0,0 +1,5 @@
+import BioSimSpace as BSS
+
+def test_tuple():
+    """Check that we can read from a tuple of files."""
+    BSS.IO.readMolecules(("test/input/ala.crd", "test/input/ala.top"))
diff --git a/test/Sandpit/Exscientia/IO/test_tuple.py b/test/Sandpit/Exscientia/IO/test_tuple.py
@@ -0,0 +1,5 @@
+import BioSimSpace.Sandpit.Exscientia as BSS
+
+def test_tuple():
+    """Check that we can read from a tuple of files."""
+    BSS.IO.readMolecules(("test/input/ala.crd", "test/input/ala.top"))