Merge pull request #905 from ComputationalCryoEM/develop

`develop` ~~> `master` v0.11.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.10.1
+current_version = 0.11.0
 commit = True
 tag = True
 

.github/workflows/long_workflow.yml

@@ -0,0 +1,39 @@
+name: ASPIRE Python Long Running Test Suite
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'develop'
+
+jobs:
+  expensive_tests:
+    runs-on: self-hosted
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[dev]"
+    - name: Customize config
+      run: |
+        echo "Setup tmp dirs and chmod so others can cleanup."
+        CI_TMP_DIR=/var/ci/tmp
+        mkdir -p ${CI_TMP_DIR}
+        chmod g+rwx  ${CI_TMP_DIR}
+        echo "Create and assign a unique temp dir to hold our config."
+        WORK_DIR=$(mktemp -d -p "${CI_TMP_DIR}")
+        echo "WORK_DIR=${WORK_DIR}"
+        echo "Stash the WORK_DIR to GitHub env so we can clean it up later."
+        echo "WORK_DIR=${WORK_DIR}" >> $GITHUB_ENV
+        echo -e "ray:\n    temp_dir: ${WORK_DIR}\n" > ${WORK_DIR}/config.yaml
+        echo -e "nufft:\n    backends: [finufft, pynfft]\n" >> ${WORK_DIR}/config.yaml
+        echo "Log the config: ${WORK_DIR}/config.yaml"
+        cat ${WORK_DIR}/config.yaml
+    - name: Run
+      run: |
+        ASPIREDIR=${{ env.WORK_DIR }} python -c \
+        "import aspire; print(aspire.config['ray']['temp_dir'])"
+        ASPIREDIR=${{ env.WORK_DIR }} pytest -m "expensive" --durations=0
+    - name: Cleanup
+      run: rm -rf ${{ env.WORK_DIR }}

.github/workflows/workflow.yml

@@ -1,8 +1,10 @@
 name: ASPIRE Python Pip CI
 
 on:
-  - push
-  - pull_request
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+  push:
+
 
 jobs:
   check:
@@ -15,26 +17,27 @@ jobs:
         python-version: '3.7'
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install tox tox-gh-actions
     - name: Run Tox Check
       run: tox -e check
 
   build:
     needs: check
     runs-on: ubuntu-latest
+    # Run on every code push, but only on review ready PRs
+    if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}    
     strategy:
       matrix:
         python-version: ['3.7', '3.8', '3.9', '3.10']
-        pyenv: [stable, dev]
+        pyenv: [pip]
         exclude:
-          # Exclude 3.7-stable so we can add pre and post tasks to that environment.
+          # Exclude 3.7-pip so we can add pre/post tasks to that environment.
           - python-version: '3.7'
-            pyenv: stable
+            pyenv: pip
         include:
-          # Re-include 3.7-stable with additional tox tasks.
+          # Re-include 3.7 with additional tox tasks.
           - python-version: '3.7'
-            pyenv: stable,docs
+            pyenv: pip,docs
 
 
     steps:
@@ -45,26 +48,68 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install tox tox-gh-actions
     - name: Test with tox
       run: tox --skip-missing-interpreters false -e py${{ matrix.python-version }}-${{ matrix.pyenv }}
     - name: Upload Coverage to CodeCov
       uses: codecov/codecov-action@v3
 
+  conda-build:
+    needs: check
+    runs-on: ${{ matrix.os }}
+    # Only run on review ready pull_requests
+    if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, ubuntu-20.04, macOS-latest, macOS-11]
+        backend: [default, openblas]
+        python-version: ['3.8']
+        include:
+          - os: ubuntu-latest
+            backend: intel
+          - os: macOS-latest
+            backend: accelerate
+          - os: windows-2019
+            backend: default
 
-  docs:
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Conda ${{ matrix.os }} Python ${{ matrix.python-version }}
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: aspire
+        environment-file: environment-${{ matrix.backend }}.yml
+        auto-activate-base: false
+    - name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
+      run: |
+        conda info
+        conda list
+        pip install -e ".[dev]"
+        pip freeze
+        python -c "import numpy; numpy.show_config()"
+    - name: Execute Pytest Conda ${{ matrix.os }} Python ${{ matrix.python-version }}
+      run: |
+        export OMP_NUM_THREADS=2
+        # -n runs test in parallel using pytest-xdist
+        pytest -n2 --durations=50 -s
+
+  # Build and Deploy production (master) docs.
+  docs_deploy:
     if: github.ref == 'refs/heads/master'
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: Setup Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.7'
+        python-version: '3.8'
     - name: Install Dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install -e ".[dev]"
     - name: Run Sphinx doc build script
       env:
@@ -77,11 +122,12 @@ jobs:
   ampere_gpu:
     needs: check
     runs-on: self-hosted
+    # Run on every code push, but only on review ready PRs
+    if: ${{ github.event_name == 'push' || github.event.pull_request.draft == false }}
     steps:
     - uses: actions/checkout@v3
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install -e ".[dev,gpu_11x]"
     - name: Customize config
       run: |
@@ -104,3 +150,30 @@ jobs:
         ASPIREDIR=${{ env.WORK_DIR }} pytest --durations=50
     - name: Cleanup
       run: rm -rf ${{ env.WORK_DIR }}
+
+  # Build branch's docs and gallery.
+  docs:
+    needs: check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.8'
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+      - name: Build Sphinx docs
+        run: |
+          make distclean
+          sphinx-apidoc -f -o ./source ../src -H Modules
+          make html
+        working-directory: ./docs
+      - name: Archive Sphinx docs
+        uses: actions/upload-artifact@v3
+        with:
+          name: sphinx-docs
+          path: docs/build
+          retention-days: 7

README.md

@@ -5,7 +5,7 @@
 [![codecov](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python/branch/master/graph/badge.svg?token=3XFC4VONX0)](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5657281.svg)](https://doi.org/10.5281/zenodo.5657281)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.10.1
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.11.0
 
 This is the Python version to supersede the [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
 
@@ -20,7 +20,7 @@ For more information about the project, algorithms, and related publications ple
 Please cite using the following DOI. This DOI represents all versions, and will always resolve to the latest one.
 
 ```
-ComputationalCryoEM/ASPIRE-Python: v0.10.1 https://doi.org/10.5281/zenodo.5657281
+ComputationalCryoEM/ASPIRE-Python: v0.11.0 https://doi.org/10.5281/zenodo.5657281
 
 ```
 
@@ -50,7 +50,7 @@ After cloning this repo, the simplest option is to use Anaconda 64-bit for your
 cd /path/to/git/clone/folder
 
 # Creates the conda environment and installs base dependencies.
-conda env create -f environment.yml --name aspire_dev
+conda env create -f environment-default.yml --name aspire_dev
 
 # Enable the environment
 conda activate aspire_dev