Merge branch 'master' into ci-fixes

kedhammar · Oct 23, 2024 · dc666f2 · dc666f2
2 parents f4f7909 + 21e4014
commit dc666f2
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Showing 11 changed files with 1,559 additions and 80 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -12,7 +12,8 @@
     "customizations": {
         "vscode": {
             "extensions": [
-                "ms-python.python"
+                "ms-python.python",
+                "vscode-es6-string-html"
             ]
         }
     },

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -36,48 +36,3 @@ jobs:
           pip install ruff
       - name: ruff --> Check code formatting
         run: ruff format --check .
-
-  # Use pipreqs to check for missing dependencies
-  pipreqs-check:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.12"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-
-      - name: Run pipreqs
-        run: |
-          pipreqs --savepath pipreqs.txt . 2>&1 | tee pipreqs_output.log
-          if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
-            missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
-            echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
-            exit 1
-          fi
-
-      - name: Compare requirements
-        run: |
-          # Extract and sort package names
-          awk -F'(=|==|>|>=|<|<=| @ )' '{gsub("-", "_", $1); print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
-          awk -F'(=|==|>|>=|<|<=| @ )' '{gsub("-", "_", $1); print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
-
-          # Compare package lists
-          missing_packages=$(comm -23 pipreqs.compare requirements.compare)
-          if [ -z "$missing_packages" ]; then
-            echo "All packages in pipreqs are listed in requirements"
-            exit 0
-          else
-            echo "Some packages in pipreqs are not listed in requirements"
-            echo ""
-            echo "=== Missing packages ==="
-            echo "$missing_packages"
-            exit 1
-          fi
diff --git a/conda_requirements.yml b/conda_requirements.yml
@@ -1,9 +1,13 @@
+channels:
+  - conda-forge
 dependencies:
   - python=3.12
-  - 'conda-forge::pango>=1.42.0'
-  - 'conda-forge::pandas>=1.3.2'
-  - conda-forge::psycopg2
-  - conda-forge::open-fonts
-  - conda-forge::xorg-libxrender
-  - conda-forge::xorg-libxext
-  - conda-forge::xorg-libxau
+  - pango>=1.42.0
+  - pandas>=1.3.2
+  - psycopg2
+  - open-fonts
+  - xorg-libxrender
+  - xorg-libxext
+  - xorg-libxau
+  - pip:
+    - '-r requirements.txt'
diff --git a/requirements.txt b/requirements.txt
@@ -14,8 +14,6 @@ nose
 numpy>=1.12.1
 oauth2>=1.9.0.post1
 openpyxl
-pandas
-psycopg2
 pycryptodome>=3.6.1
 pyparsing>=2.2.0
 python-dateutil>=2.7.5

diff --git a/requirements_dev.txt b/requirements_dev.txt
@@ -1,4 +1,3 @@
 ipdb
-pipreqs
 ruff
 selenium
diff --git a/run_dir/design/element_flowcell.html b/run_dir/design/element_flowcell.html
@@ -1,8 +1,16 @@
 {% extends 'base.html' %}
 {% block stuff %}
-<div id="page_content">
-    <h1>Element BioSciences (AVITI) run <span id="page_title"></span></h1>
-    <div>Under construction. This page should contain information about a single element biosciences run.</div>
+<div id="element_vue_app">
+    <v-element-flowcell ngi_run_id="{{ngi_run_id}}"/>
 </div>
+{% end %}
+
+{% block js %}
+
+<script src="/static/js/vue.v3.2.47.global.prod.js"></script>
+<script src="/static/js/axios.v1.3.4.min.js"></script>
+<script src="https://code.highcharts.com/highcharts.js"></script>
+<script src="/static/js/element_flowcell.js?v={{ gs_globals['git_commit'] }}"></script>
 
 {% end %}
+
diff --git a/run_dir/design/element_flowcells.html b/run_dir/design/element_flowcells.html
@@ -8,8 +8,8 @@ <h1>
 
         <thead style="vertical-align: top">
             <tr class="sticky darkth">
+                <th class="sort" data-sort="ngi_run_id">NGI Run ID</th>
                 <th class="sort" data-sort="start_date">Start date</th>
-                <th class="sort" data-sort="run_name">Run name</th>
                 <th class="sort" data-sort="run_type">Run type</th>
                 <th class="sort" data-sort="side">Side</th>
                 <th class="sort" data-sort="cycles">Cycles</th>
@@ -21,8 +21,8 @@ <h1>
         </thead>
         <tfoot>
             <tr class="darkth">
+                <th class="sort searchable" data-sort="ngi_run_id">NGI Run ID</th>
                 <th class="sort searchable" data-sort="start_date">Start date</th>
-                <th class="sort searchable" data-sort="run_name">Run name</th>
                 <th class="sort searchable" data-sort="run_type">Run type</th>
                 <th class="sort searchable" data-sort="side">Side</th>
                 <th class="sort searchable" data-sort="cycles">Cycles</th>
@@ -35,9 +35,8 @@ <h1>
         <tbody class="list">
             {% for onefc in element_fcs %}
                 <tr>
-                    <td class="start_date">{{ onefc.key[:10] }}</td>
-                    <td class = run_name>
-                        <a class="text-decoration-none" href="/flowcells_element/{{ onefc.id }}">{{ onefc.value['RunName'] }}</a>
+                    <td class="ngi_run_id">
+                        <a class="text-decoration-none" href="/flowcells_element/{{ onefc.key }}">{{ onefc.key }}</a>
                         {% if onefc.value.get('Outcome') == 'OutcomeCompleted' %}
                             <abbr title="Run completed"><span class="fa fa-check-circle"></span></abbr>
                         {% elif onefc.value.get('Outcome') == 'ongoing' %}
@@ -48,26 +47,27 @@ <h1>
                            <abbr title="Run failed"><span class="fa fa-file-dashed-line"></span></abbr>
                         {% end %}
                     </td>
+                    <td class="start_date">{{ onefc.key[:8] }}</td>
                     <td class="run_type">
-                        {{ onefc.value["RunType"] }}
+                        {{ onefc.value.get("RunType") }}
                     </td>
                     <td class="side">
-                        {{ onefc.value["Side"] }}
+                        {{ onefc.value.get("Side") }}
                     </td>
                     <td class="cycles">
-                        {{ onefc.value["Cycles"] }}
+                        {{ onefc.value.get("Cycles") }}
                     </td>
                     <td class="throughput_selection">
-                        {{ onefc.value["ThroughputSelection"] }}
+                        {{ onefc.value.get("ThroughputSelection") }}
                     </td>
                     <td class="kit_configuration">
-                        {{ onefc.value["KitConfiguration"] }}
+                        {{ onefc.value.get("KitConfiguration") }}
                     </td>
                     <td class="chemistry_version">
-                        {{ onefc.value["ChemistryVersion"] }}
+                        {{ onefc.value.get("ChemistryVersion") }}
                     </td>
                     <td class="outcome text-center">
-                        {{ onefc.value["Outcome"] }}
+                        {{ onefc.value.get("Outcome") }}
                     </td>
                 </tr>
             {% end %}

diff --git a/run_dir/design/pricing_preview.html b/run_dir/design/pricing_preview.html
@@ -10,7 +10,6 @@
 
 {% block js %}
 
-<!-- development version, includes helpful console warnings -->
 <script src="/static/js/vue.v3.2.47.global.prod.js"></script>
 <script src="/static/js/axios.v1.3.4.min.js"></script>
 <script src="/static/js/dataTables-extensions-1.13.6.min.js"></script>