Merge remote-tracking branch 'origin/master'

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1,2 +1,4 @@
 # Auto detect text files and perform LF normalization
 * text=auto
+
+.git_archival.txt export-subst

.github/pull_request_template.md

@@ -0,0 +1,19 @@
+# Description
+
+Please include a summary of the changes and the related issue. Please also
+include relevant motivation and context. Please list issues fixed or closed by
+This PR.
+
+- Fixes #000: How this PR fixes the issue
+  - `path/file.py`: Description of the change
+  - `path/file.py`: Description of the change
+- Fixes #000: How this PR fixes the issue
+  - `path/file.py`: Description of the change
+  - `path/file.py`: Description of the change
+
+# Checklist:
+
+- [ ] This PR should be accompanied by a release: (yes/no/unsure)
+- [ ] (If release) I have updated the `CITATION.cff`
+- [ ] I have updated the `CHANGELOG.md`
+- [ ] I have added/edited docs/notebooks to reflect the changes

.github/workflows/publish-docs.yml

@@ -0,0 +1,47 @@
+name: Publish docs
+on:
+  push:
+    tags: # See PEP 440 for valid version format
+      - "*.*.*" # For docs bump, use X.X.XaX
+    branches:
+      - test_branch
+
+permissions:
+  contents: write
+  pull-requests: write
+  issues: write
+  repository-projects: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    env:
+      REPO_OWNER: ${{ github.repository_owner }}
+    permissions:
+      contents: write
+      issues: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          fetch-depth: 0
+
+      - name: Set up Python runtime
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Setup - pip & config
+        run: |
+          pip install .[docs]
+          git config user.name 'github-actions[bot]' && git config user.email 'github-actions[bot]@users.noreply.github.com'
+
+      - name: Deploy
+        run: |
+          echo "OWNER: ${REPO_OWNER}"
+          bash ./docs/build-docs.sh push $REPO_OWNER
+        env:
+          USERNAME: github-actions[bot]
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/workflow.yml → .github/workflows/test-conda.yml

@@ -1,4 +1,4 @@
-name: Run tests
+name: Test conda env and run tests
 
 on:
   push:
@@ -17,16 +17,6 @@ jobs:
     env:
       OS: ${{ matrix.os }}
       PYTHON: '3.8'
-    #   SPYGLASS_BASE_DIR: ./data
-    #   KACHERY_STORAGE_DIR: ./data/kachery-storage
-    #   DJ_SUPPORT_FILEPATH_MANAGEMENT: True
-    # services:
-    #   datajoint_test_server:
-    #     image: datajoint/mysql
-    #     ports:
-    #     - 3306:3306
-    #     options: >-
-    #       -e MYSQL_ROOT_PASSWORD=tutorial
     steps:
     - name: Cancel Workflow Action
       uses: styfle/cancel-workflow-action@0.11.0
@@ -46,12 +36,20 @@ jobs:
         environment-file: environment.yml
         miniforge-variant: Mambaforge
         miniforge-version: latest
-    - name: Install test requirements
-      run: |
-        pip install -r requirements-dev.txt
     - name: Install spyglass
       run: |
-        pip install -e .
+        pip install -e .[test]
+    - name: Download data
+      env:
+        UCSF_BOX_TOKEN: ${{ secrets.UCSF_BOX_TOKEN }}
+        UCSF_BOX_USER: ${{ secrets.UCSF_BOX_USER }}
+        WEBSITE: ftps://ftp.box.com/trodes_to_nwb_test_data/minirec20230622.nwb
+        RAW_DIR: /home/runner/work/spyglass/spyglass/tests/_data/raw/ 
+      run: |
+        mkdir -p $RAW_DIR
+        wget --recursive --no-verbose --no-host-directories --no-directories \
+        --user $UCSF_BOX_USER --password $UCSF_BOX_TOKEN \
+        -P $RAW_DIR $WEBSITE
     - name: Run tests
       run: |
         pytest -rP  # env vars are set within certain tests

.github/workflows/test-package-build.yml

@@ -0,0 +1,98 @@
+name: Test package building
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - master
+      - maint/*
+defaults:
+  run:
+    shell: bash
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - run: pip install --upgrade build twine
+      - name: Build sdist and wheel
+        run: python -m build
+      - run: twine check dist/*
+      - name: Upload sdist and wheel artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist/
+      - name: Build git archive
+        run: mkdir archive && git archive -v -o archive/archive.tgz HEAD
+      - name: Upload git archive artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: archive
+          path: archive/
+  test-package:
+    runs-on: ubuntu-latest
+    needs: [build]
+    strategy:
+      matrix:
+        package: ['wheel', 'sdist', 'archive']
+    steps:
+      - name: Download sdist and wheel artifacts
+        if: matrix.package != 'archive'
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+      - name: Download git archive artifact
+        if: matrix.package == 'archive'
+        uses: actions/download-artifact@v3
+        with:
+          name: archive
+          path: archive/
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Update pip
+        run: pip install --upgrade pip
+      - name: Install wheel
+        if: matrix.package == 'wheel'
+        run: pip install dist/*.whl
+      - name: Install sdist
+        if: matrix.package == 'sdist'
+        run: pip install dist/*.tar.gz
+      - name: Install archive
+        if: matrix.package == 'archive'
+        run: pip install archive/archive.tgz
+      # - name: Install test extras
+      #   run: pip install spyglass[test]
+      # - name: Run tests
+      #   run: pytest --doctest-modules -v --pyargs spyglass
+  publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    needs: [test-package]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/spyglass-neuro
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -6,23 +6,7 @@ mysql_config
 
 # Notebooks
 *.ipynb
-
-!notebooks/00_intro.ipynb
-!notebooks/01_spikesorting.ipynb
-!notebooks/02_curation.ipynb
-!notebooks/03_lfp.ipynb
-!notebooks/04_Trodes_position.ipynb
-!notebooks/05_DLC_from_scratch.ipynb
-!notebooks/06_DLC_from_dir.ipynb
-!notebooks/4_position_info.ipynb
-!notebooks/07_linearization.ipynb
-!notebooks/08_Extract_Mark_indicators.ipynb
-!notebooks/09_Decoding_with_GPUs_on_the_GPU_cluster.ipynb
-!notebooks/10_1D_Clusterless_Decoding.ipynb
-!notebooks/11_2D_Clusterless_Decoding.ipynb
-!notebooks/12_Ripple_Detection.ipynb
-!notebooks/13_Theta_phase_and_power.ipynb
-
+!notebooks/[0-9]*.ipynb
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -92,9 +76,6 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 target/
 
@@ -137,9 +118,6 @@ venv.bak/
 # Rope project settings
 .ropeproject
 
-# mkdocs documentation
-/site
-
 # mypy
 .mypy_cache/
 .dmypy.json
@@ -165,7 +143,6 @@ dmypy.json
 temp_nwb/*s
 
 *.mp4
-dj_local_conf.json
 *.png
 *.npy
 *.nc
@@ -174,8 +151,27 @@ dj_local_conf.json
 *.json
 *.gz
 *.pdf
+*.lock
+*.npz
+*.xz
+*.zip
+*.pb
+*.pem
+dj_local_conf*
+!dj_local_conf_example.json
 
 !/.vscode/extensions.json
 !/.vscode/settings.json
-!/notebooks/dlc_scratch.png
-!/notebooks/dlc_existing.png
+!/notebooks/notebook-images/dlc_scratch.png
+!/notebooks/notebook-images/dlc_existing.png
+
+# Documentation
+docs/site/
+docs/src/CHANGELOG.md
+docs/src/LICENSE.md
+docs/src/notebooks/
+!docs/src/images/*png
+temp*
+
+# Version
+_version.py

.markdownlint.yaml

@@ -0,0 +1,13 @@
+# https://github.com/DavidAnson/markdownlint
+# https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
+MD007: false # permit indenting 4 spaces instead of 2
+MD013:
+    line_length: "80" # Line length limits
+    tables: false # disable for tables
+    code_blocks: false # disable for code blocks
+MD025: false # permit adjacent headings
+MD026: false # permit trailing punctuation in headings
+MD033: # HTML elements allowed
+    allowed_elements:
+        - "img"
+MD034: false # Bare URLs OK