Merge branch 'main' into add-project-0978E406-3ADD-477B-87C3-F9D7846D…

…C52E
evangeline-corcoran · Aug 8, 2024 · 61473ff · 61473ff
2 parents ab71e40 + 245870e
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -263,6 +263,20 @@
         "promotion",
         "blog"
       ]
+    },
+    {
+      "login": "aldenc",
+      "name": "Alden Conner",
+      "avatar_url": "https://avatars.githubusercontent.com/u/20688591?v=4",
+      "profile": "https://github.com/aldenc",
+      "contributions": [
+        "ideas",
+        "doc",
+        "design",
+        "eventOrganizing",
+        "promotion",
+        "projectManagement"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.github/ISSUE_TEMPLATE/new-datasource.md b/.github/ISSUE_TEMPLATE/new-datasource.md
@@ -5,20 +5,27 @@ title: '[DATA]'
 labels: ["catalog", "data"]
 ---
 
+It is recommended that you first read the information on how to [submit a datasource](https://scivision.readthedocs.io/en/latest/contributing.html#preparing-a-dataset-for-inclusion-in-the-catalog)), and how to ensure your [datasource is in the correct format](https://scivision.readthedocs.io/en/latest/data_repository_template.html)).
+
+
 ## Details
 
-<!-- Please add details about the dataset when opening the issue -->
+<!-- Please add a brief description of the dataset when opening the issue -->
+
+
 
-Name, description, link etc.
+## Process checklist
 
+<!-- These tasks to be addressed after opening the issue - when the dataset has been added to the catalog, the issue can be closed. -->
 
-## Checklist
+(More details can be found in the links above)
 
-<!-- These tasks to be addressed after opening the issue - when they are all done, the issue can be closed -->
+- [ ] Data is publicly accessible with a stable link (and suitably licenced)
+- [ ] Optional: The data has an associated Scivision data yml file (or data loader/plugin)
+- [ ] Catalog metadata .json file created using https://sci.vision/new-datasource
+- [ ] Thumbnail image created
 
-([Full documentation on creating a datasource](https://scivision.readthedocs.io/en/latest/data_repository_template.html))
+Then you have two choices (select the one you will follow):
+- [ ] Attach the .json file and the thumbnail to this issue. If you choose to do this, a scivision maintainer will open a PR on your behalf to add the dataset to the catalog. They will notify you when that has been done.
+- [ ] Open a PR, and add the .json file details / thumbnail to the datasource catalog, as described in https://scivision.readthedocs.io/en/latest/contributing.html#manual-steps-for-adding-a-dataset. Request a review from the Scivision maintainers.
 
-- [ ] Publicly accessible with a stable link (and suitably licenced)
-- [ ] The data has an associated scivision data yml file (or data loader/plugin)
-- [ ] Catalog metadata added (can open a pull request with https://sci.vision/#/new-datasource)
-- [ ] Thumbnail image uploaded
diff --git a/.github/ISSUE_TEMPLATE/new-model.md b/.github/ISSUE_TEMPLATE/new-model.md
@@ -5,20 +5,26 @@ title: '[MODEL]'
 labels: ["catalog", "model"]
 ---
 
-## Details
+It is recommended that you first read the information on how to [submit a model](https://scivision.readthedocs.io/en/latest/contributing.html#preparing-a-model-for-inclusion-in-the-catalog)), and how to ensure your [model is in the correct format](https://scivision.readthedocs.io/en/latest/model_repository_template.html)).
 
-<!-- Please add details about the model below, when opening the issue -->
+## Details
 
-Name, description, link etc.
+<!-- Please add a brief description of the model below, when opening the issue -->
 
 
 ## Checklist
 
-<!-- These tasks to be addressed after opening the issue - when they are all done, the issue can be closed -->
+<!-- These tasks to be addressed after opening the issue - when the model has been added to the catalog, the issue can be closed. -->
 
-([Full documentation on creating a model](https://scivision.readthedocs.io/en/latest/model_repository_template.html))
+(More details can be found in the links above)
 
 - [ ] Publicly accessible model repository (e.g. on GitHub), with a suitable software licence
-- [ ] The model has an associated scivision model yml file
-- [ ] Catalog metadata added (can open a pull request with https://sci.vision/#/new-model)
-- [ ] Thumbnail image uploaded
+- [ ] Optional: The model has an associated Scivision model yml file
+- [ ] Catalog metadata .json file created using https://sci.vision/new-model
+- [ ] Thumbnail image created
+
+Then you have two choices (select the one you will follow):
+- [ ] Attach the .json file and the thumbnail to this issue. If you choose to do this, a scivision maintainer will open a PR on your behalf to add the model to the catalog. They will notify you when that has been done
+- [ ] Open a PR, and add the .json file details / thumbnail to the model catalog, as described in https://scivision.readthedocs.io/en/latest/contributing.html#manual-steps-for-adding-a-model. Request a review from the Scivision maintainers.
+
+
diff --git a/.github/ISSUE_TEMPLATE/new-project.md b/.github/ISSUE_TEMPLATE/new-project.md
@@ -0,0 +1,29 @@
+---
+name: "New Project"
+about: "A suggestion for a project to add to the catalog"
+title: '[PROJECT]'
+labels: ["catalog", "project"]
+---
+
+It is recommended that you first read the information on how to [submit a project](https://scivision.readthedocs.io/en/latest/contributing.html#preparing-a-project-for-inclusion-in-the-catalog)).
+
+## Details
+
+<!-- Please add a brief description of the project below, and the related model(s) / dataset(s), when opening the issue -->
+
+
+## Checklist
+
+<!-- These tasks to be addressed after opening the issue - when the project has been added to the catalog, the issue can be closed. -->
+
+(More details can be found in the link above)
+
+- [ ] Associated model(s) / dataset(s) in the Scivision catalog
+- [ ] Catalog metadata .json file created using https://sci.vision/new-project
+- [ ] Thumbnail image created
+
+Then you have two choices (select the one you will follow):
+- [ ] Attach the .json file and the thumbnail to this issue. If you choose to do this, a scivision maintainer will open a PR on your behalf to add the project to the catalog. They will notify you when that has been done
+- [ ] Open a PR, and add the .json file details / thumbnail to the project catalog, as described in https://scivision.readthedocs.io/en/latest/contributing.html#manual-steps-for-adding-a-project. Request a review from the Scivision maintainers.
+
+
diff --git a/.github/workflows/check-catalogs.yml b/.github/workflows/check-catalogs.yml
@@ -1,15 +1,19 @@
-name: Check catalogs
+name: Auto-update check_datasets.js
 on:
+  workflow_dispatch:
   schedule:
     - cron:  '18 3 * * *'
 
 jobs:
   check-catalogs:
+    name: Check catalogs and create check_datasets.js file
     runs-on: ubuntu-latest
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          ref: catalog-validation 
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
@@ -20,16 +24,16 @@ jobs:
       - name: Check data catalog
         run: scivision-check-datasets
       - name: Store artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: check-datasets-report
-          path: check_datasets.csv
-      - name: Create Release
-        uses: ncipollo/release-action@v1
-        with:
-          tag: catalog-checks-report-latest-release
-          name: Catalog checks report
-          commit: ${{ github.ref }}
-          allowUpdates: true
-          removeArtifacts: true
-          artifacts: check_datasets.js
+          path: check_datasets.js
+      - name: Update check_datasets.js in frontend repository
+        run: |
+          mv -f check_datasets.js frontend/src/consts/check_datasets.js
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git pull origin catalog-validation
+          git add .
+          git commit -m "auto-update via GH Action"
+          git push origin catalog-validation
diff --git a/.github/workflows/check-models.yml b/.github/workflows/check-models.yml
@@ -0,0 +1,41 @@
+name: Auto-update check_models.js
+on:
+  workflow_dispatch:
+  schedule:
+    - cron:  '18 3 * * *'
+jobs:
+  check-models:
+    name: Check models and create check_models.js file
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: catalog-validation 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
+      - name: Install Scivision
+        run: pip install -e .
+      - name: Install chardet
+        run: pip install chardet 
+      - name: Check model catalog
+        run: scivision-check-models
+      - name: Store artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: check-models-report
+          path: check_models.js
+      - name: Update check_models.js in frontend repository
+        run: |
+          mv -f check_models.js frontend/src/consts/check_models.js
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git pull origin catalog-validation
+          git add .
+          git commit -m "auto-update via GH Action"
+          git push origin catalog-validation
+  
diff --git a/.github/workflows/frontend.yml b/.github/workflows/frontend.yml
@@ -4,14 +4,32 @@ on: [push, pull_request]
 jobs:
   build-and-deploy-if-main:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:    
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
+      with:
+        ref: catalog-validation
+        fetch-depth: 0
+
+    - name: Update branch
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        git checkout main
+        git fetch origin
+        git checkout catalog-validation
+        git pull
+        git merge origin/main
+        git push origin catalog-validation
 
     - name: Install node
-      uses: actions/setup-node@v1
+      uses: actions/setup-node@v4
       with:
-        node-version: '16.15.1'
+        node-version: 20
+        cache: "npm"
+        cache-dependency-path: "./frontend/package-lock.json"
 
     - name: Setup python
       uses: actions/setup-python@v4
@@ -28,19 +46,14 @@ jobs:
 
     - name: Build
       working-directory: frontend
-      env:
-        CI: ""
-      run: |
-        npm run build
-        pwd
-        ls
+      run: npm run build && cp ./dist/index.html ./dist/404.html && cp ./CNAME ./dist/CNAME
 
     - name: Deploy
       uses: JamesIves/github-pages-deploy-action@v4.2.2
       if: github.ref == 'refs/heads/main' && github.event_name == 'push'
       with:
         token: ${{ secrets.GITHUB_TOKEN }}
         branch: gh-pages
-        folder: frontend/build
+        folder: frontend/dist
         clean: true
 
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -25,6 +25,6 @@ jobs:
         build
     - name: Publish distribution 📦 to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
     - id: black
       pass_filenames: true
       args: [--line-length=79]
--   repo: https://gitlab.com/pycqa/flake8
+-   repo: https://github.com/PyCQA/flake8
     rev: 3.8.3
     hooks:
     - id: flake8

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,50 @@
+cff-version: 1.2.0
+title: scivision
+message: "If you use this software, please cite it using the metadata from this file."
+type: software
+authors:
+  - given-names: Sebastian
+    family-names: Ahnert
+  - given-names: Meghna
+    family-names: Asthana
+    orcid: 'https://orcid.org/0000-0002-6101-8904'
+  - given-names: Edward Jonathan
+    family-names: Chalstrey
+    orcid: 'https://orcid.org/0000-0003-2560-1294'
+  - given-names: Alejandro
+    family-names: Coca-Castro
+    orcid: 'https://orcid.org/0000-0002-9264-1539'
+  - given-names: Alden
+    family-names: Conner
+    orcid: 'https://orcid.org/0000-0003-0927-2267'
+  - given-names: Evangeline Mae
+    family-names: Corcoran
+    orcid: 'https://orcid.org/0000-0003-0321-009X'
+  - given-names: Beatriz
+    family-names: Costa-Gomes
+    orcid: 'https://orcid.org/0000-0002-1073-8442'
+  - given-names: Isabel S.
+    family-names: Fenton
+    orcid: 'https://orcid.org/0000-0001-7174-0725'
+  - given-names: J. Scott
+    family-names: Hosking
+    orcid: 'https://orcid.org/0000-0002-3646-3504'
+  - given-names: Alan R
+    family-names: Lowe
+    orcid: 'https://orcid.org/0000-0002-0558-3597'
+  - given-names: Oliver
+    family-names: Strickson
+    orcid: 'https://orcid.org/0000-0002-8177-5582'
+  - given-names: Samuel
+    family-names: Tonks
+    orcid: 'https://orcid.org/0009-0008-1408-1493'
+repository-code: 'https://github.com/alan-turing-institute/scivision'
+url: 'https://sci.vision/'
+identifiers:
+  - type: doi
+    value: '10.5281/zenodo.10792860'
+keywords:
+  - computer vision
+  - image analysis
+license: BSD-3-Clause
+