Merge pull request #2 from ACCESS-NRI/CD

added cd to upload to conda
ACCESS-NRI · Jul 2, 2024 · 5e78942 · 5e78942
2 parents c581e28 + d1d36ea
commit 5e78942
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Showing 3 changed files with 42 additions and 8 deletions.
diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
@@ -0,0 +1,37 @@
+name: CD
+
+on:
+  push:
+    branches:
+        - master
+
+env:
+  PY_VERSION: 3.12
+
+jobs:
+
+  conda:
+    name: Build with conda and upload
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ env.PY_VERSION }}
+          environment-file: conda/environment.yml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Build and upload the conda package
+        uses: uibcdf/action-build-and-upload-conda-packages@c6e7a90ad5e599d6cde76e130db4ee52ad733ecf
+        with:
+          meta_yaml_dir: conda
+          python-version: ${{ env.PY_VERSION }}
+          user: accessnri
+          label: main
+          token: ${{ secrets.anaconda_token }}
diff --git a/conda/environment.yml b/conda/environment.yml
@@ -1,14 +1,12 @@
 name: ncigrafana
 
 channels:
-    - coecms
     - conda-forge
     - defaults
 
 dependencies:
     - python
     - sqlite
-    - dataset
     - pandas
     - matplotlib
     - numpy

diff --git a/ncigrafana/UsageDataset.py b/ncigrafana/UsageDataset.py
@@ -421,11 +421,10 @@ def getusage(self, year, quarter, datafield='usage_su', namefield='user+name'):
 
         # Pivot makes columns of all the individuals, rows are indexed by date
         try:
-            df = pd.read_sql_query(qstring.format(namefield=name_sql,
+            df = pd.DataFrame(data=list(self.db.query(qstring.format(namefield=name_sql,
                                                   datafield=datafield,
                                                   start=startdate,
-                                                  end=enddate),
-                                                  self.db.executable).pivot_table(index='Date',
+                                                  end=enddate)))).pivot_table(index='Date',
                                                                                   columns='Name',
                                                                                   fill_value=0)
         except:
@@ -470,14 +469,14 @@ def getstorage(self, project, year, quarter, systemname, storagepoint='scratch',
 
         # Pivot makes columns of all the individuals, rows are indexed by date
         try:
-            df = pd.read_sql_query(qstring.format(namefield=name_sql,
+            df = pd.DataFrame(data=list(self.db.query(qstring.format(namefield=name_sql,
                                                   datafield=datafield,
                                                   table=table,
                                                   project_id=project_id,
                                                   storagepoint_id=storagepoint_id,
                                                   start=startdate,
-                                                  end=enddate), 
-                                   self.db.executable).pivot_table(index='Date', columns='Name', fill_value=0)
+                                                  end=enddate)))).pivot_table(index='Date', 
+                                                                              columns='Name', fill_value=0)
         except:
             print("No data available for {}".format(storagepoint))
             return None