diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml index e4ee051bf..dd7a77988 100644 --- a/.github/workflows/Build-and-deploy-mac.yml +++ b/.github/workflows/Build-and-deploy-mac.yml @@ -33,6 +33,9 @@ jobs: - name: Install package.json modules and their dependencies run: npm install --ignore-scripts + - name: Remove bad sonpy file (might make Spike2 format unusable on Mac - should exclude from selection) + run: rm -f /usr/local/miniconda/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so + - uses: apple-actions/import-codesign-certs@v1 with: # https://developer.apple.com/account/resources/certificates/add @@ -56,5 +59,4 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} appleId: ${{ secrets.APPLE_ID }} # currently this is set to Ryan's Apple ID and password appleIdPassword: ${{ secrets.APPLE_PASSWORD }} - run: | - npm run deploy:mac + run: npm run deploy:mac diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml index e2e983010..5fbea858d 100644 --- a/.github/workflows/pyflask-build-and-dist-tests.yml +++ b/.github/workflows/pyflask-build-and-dist-tests.yml @@ -83,6 +83,10 @@ jobs: - run: npm ci + # fix for macos build + - if: matrix.os == 'macos-latest' + run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so + - name: Build PyFlask distribution run: npm run build:flask:${{ matrix.shorthand }} diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml index 87a4fe4a1..d55ea40bf 100644 --- a/environments/environment-Linux.yml +++ b/environments/environment-Linux.yml @@ -1,31 +1,22 @@ name: nwb-guide channels: - - defaults - conda-forge + - defaults dependencies: - - python = 3.9.17 - - PyInstaller = 4.7 - - nodejs = 16.14.2 - - libgcc = 7.2.0 - - git = 2.20.1 + - python = 3.9.18 + - PyInstaller = 5.13.0 + - nodejs = 18.16.1 + - numcodecs = 0.11.0 + # install these from conda-forge so that dependent packages get included in the distributable + - jsonschema = 4.18.0 # installs jsonschema-specifications + - pydantic[email] = 2.0.2 # installs email-validator - pip - pip: - - chardet == 4.0.0 - - pandas == 1.4.2 - - openpyxl == 3.0.3 - - pennsieve == 6.1.2 - - configparser == 4.0.2 - - python-docx == 0.8.10 - - xlrd == 1.2.0 - - biopython == 1.79 - - flask == 2.0.2 - - flask_restx - - protobuf == 3.20.0 - - gevent == 21.12.0 - - werkzeug == 2.0.2 - - opencv-python == 4.5.3.56 + - chardet == 5.1.0 + - configparser == 6.0.0 + - flask == 2.3.2 + - flask-cors == 4.0.0 + - flask_restx == 1.1.0 - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - hdmf >= 3.7.0 - - pytest == 7.2.2 + - pytest == 7.4.0 - pytest-cov == 4.1.0 - - flask-cors === 3.0.10 diff --git a/environments/environment-MAC-arm64.yml b/environments/environment-MAC-arm64.yml index 4c0ca3ae3..6e4508a61 100644 --- a/environments/environment-MAC-arm64.yml +++ b/environments/environment-MAC-arm64.yml @@ -3,21 +3,23 @@ channels: - conda-forge - defaults dependencies: - - python = 3.9.17 + - python = 3.9.18 - PyInstaller = 5.13.0 - nodejs = 18.16.1 - numcodecs = 0.11.0 - lxml = 4.9.3 # pypi build fails due to x64/arm64 mismatch so install from conda-forge - pyedflib = 0.1.32 # pypi build fails due to x64/arm64 mismatch so install from conda-forge - - jsonschema = 4.18.0 # this installs jsonschema-specifications which is needed for validation - - pydantic[email] = 2.0.2 # email validator is used by dandi - numpy # may have x64/arm64 mismatch issues so install from conda-forge + # install these from conda-forge so that dependent packages get included in the distributable + - jsonschema = 4.18.0 # installs jsonschema-specifications + - pydantic[email] = 2.0.2 # installs email-validator - pip - pip: - chardet == 5.1.0 - configparser == 6.0.0 - flask == 2.3.2 - - flask_restx == 1.1.0 - flask-cors == 4.0.0 - - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[ecephys] + - flask_restx == 1.1.0 + - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - pytest == 7.4.0 + - pytest-cov == 4.1.0 diff --git a/environments/environment-MAC.yml b/environments/environment-MAC.yml index cd76d4596..d55ea40bf 100644 --- a/environments/environment-MAC.yml +++ b/environments/environment-MAC.yml @@ -1,22 +1,22 @@ name: nwb-guide channels: - - defaults - conda-forge + - defaults dependencies: - - python = 3.9.17 - - nodejs = 18.16.1 + - python = 3.9.18 - PyInstaller = 5.13.0 + - nodejs = 18.16.1 - numcodecs = 0.11.0 - - jsonschema = 4.18.0 # this installs jsonschema-specifications which is needed for validation - - pydantic[email] = 2.0.2 # email validator is used by dandi + # install these from conda-forge so that dependent packages get included in the distributable + - jsonschema = 4.18.0 # installs jsonschema-specifications + - pydantic[email] = 2.0.2 # installs email-validator - pip - pip: - chardet == 5.1.0 - configparser == 6.0.0 - flask == 2.3.2 - - flask-cors === 3.0.10 + - flask-cors == 4.0.0 - flask_restx == 1.1.0 - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full] - - hdmf >= 3.7.0 - - pytest == 7.2.2 + - pytest == 7.4.0 - pytest-cov == 4.1.0 diff --git a/package.json b/package.json index 6d545d081..3ea6741de 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "nwb-guide", "productName": "NWB GUIDE", - "version": "0.0.4", + "version": "0.0.5", "description": "", "main": "./build/main/main.js", "scripts": { @@ -15,9 +15,9 @@ "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win", "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac", "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux", - "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator", + "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator", "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.", - "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys", + "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:.", "build:electron:win": "electron-builder build --win --publish never", "build:electron:mac": "electron-builder build --mac --publish never", "build:electron:linux": "electron-builder build --linux --publish never",