NAVDAT Backend and Rahul User Stories

.github/workflows/test_navdat.yml

@@ -0,0 +1,36 @@
+name: navdat.py test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install . -r requirements.extras.txt
+
+      - name: Test NAVDAT Backend
+        run: |
+          pip install pytest
+          pytest dsi/backends/tests/test_navdat.py -vv -s --maxfail=1 --full-trace --log-cli-level=INFO
+        env:
+          PYTHONUNBUFFERED: 1

.github/workflows/test_user_stories.yml

@@ -0,0 +1,61 @@
+name: User Stories test
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    # strategy:
+    #   matrix:
+    #     python-version: ['3.11']
+
+    steps:
+    - uses: actions/checkout@v5
+    # - name: Set up Python ${{ matrix.python-version }}
+    #   uses: actions/setup-python@v6
+    #   with:
+    #     python-version: ${{ matrix.python-version }}
+    - name: Check user stories structure
+      shell: bash
+      run: |
+        set -euo pipefail
+
+        [[ -d tools ]] || {
+          echo "::error::tools/ directory does not exist."
+          exit 1
+        }
+
+        failed=0
+
+        while IFS= read -r -d '' tool_dir; do
+          has_readme=0
+
+          for file in "$tool_dir"/*; do
+            [[ -f "$file" ]] || continue
+
+            filename="${file##*/}"
+            if [[ "${filename,,}" == "readme.md" ]]; then
+              has_readme=1
+              break
+            fi
+          done
+
+          if [[ "$has_readme" -eq 0 ]]; then
+            echo "::error file=$tool_dir::A README file is required (README.md or readme.md)."
+            failed=1
+          fi
+
+          if [[ ! -f "$tool_dir/requirements.txt" ]]; then
+            echo "::error file=$tool_dir::requirements.txt is required."
+            failed=1
+          fi
+        done < <(find tools -mindepth 1 -maxdepth 1 -type d -print0)
+
+        exit "$failed"

docs/backends.rst

@@ -105,4 +105,12 @@ RCSBPDB (Read-only)
 
 .. automodule:: dsi.backends.rcsbpdb
    :members: RCSBPDB
+   :special-members: __init__
+
+
+NAVDAT (Read-only)
+-------------------
+
+.. automodule:: dsi.backends.navdat
+   :members: NAVDAT
    :special-members: __init__

docs/cr_intro.rst

@@ -51,6 +51,7 @@ Webserver Backends - Create a connection to a remote data platform for users to
   - NDP (Read-only): Connection to data on the `National Data Platform <https://nationaldataplatform.org/>`_
   - Denodo (Read-only): Connection to a specific `Denodo Data Catalog <https://www.denodo.com/>`_ instance. 
   - RCSBPDB (Read-only): Connection to data on the `Research Collaboratory for Structural Bioinformatics Protein Data Bank <https://www.rcsb.org/>`_
+  - NAVDAT (Read-only): Connection to data on the `North American Volcanic and Intrusive Rock Database <https://www.navdat.org/>`_
 
 DSI Core
 ~~~~~~~~

docs/introduction.rst

@@ -114,6 +114,7 @@ Webserver Backends - Create a connection to a remote data platform for users to
   - NDP (Read-only): Connection to data on the `National Data Platform <https://nationaldataplatform.org/>`_
   - Denodo (Read-only): Connection to a specific `Denodo Data Catalog <https://www.denodo.com/>`_ instance. 
   - RCSBPDB (Read-only): Connection to data on the `Research Collaboratory for Structural Bioinformatics Protein Data Bank <https://www.rcsb.org/>`_
+  - NAVDAT (Read-only): Connection to data on the `North American Volcanic and Intrusive Rock Database <https://www.navdat.org/>`_
 
 DSI Core
 ~~~~~~~~