Merge branch 'main' into dandi-api-key-instructions

.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

.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 }}
 

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

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

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

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",