Merge branch 'main' into add-release-pr-trigger

.github/workflows/build_test.yml

@@ -22,7 +22,6 @@ jobs:
     permissions:
       contents: read
       packages: write
-      pull-requests: write
 
     strategy:
       fail-fast: false
@@ -59,21 +58,45 @@ jobs:
         continue-on-error: true
         uses: docker/build-push-action@v5
         with:
-          cache-from: type=registry,ref=ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache
-          cache-to: type=registry,ref=ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache,mode=max
+          cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache
+          cache-to: type=registry,ref=ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache,mode=max
           file: docker/Dockerfile
           build-args: |
             pkg_mgr=${{ matrix.pkg_mgr }}
             ubuntu_version=${{ matrix.ubuntu_versions }}
             cycamore_tag=${{ matrix.cycamore_tag }}
 
-      - name: PR Comment
-        if: ${{ github.event_name == 'pull_request' }}
-        uses: thollander/actions-comment-pull-request@v2
+      - name: Export Environment Variables
+        if: github.event_name == 'pull_request'
+        run: |
+          echo "BUILD_STATUS=${{steps.build-cymetric.outcome == 'success' && '**Success** :white_check_mark:' || 
+          steps.build-cymetric.outcome == 'failure' && '**Failure** :x:' || 
+          '**Skipped due to upstream failure** :warning:'}}" >> "$GITHUB_ENV"
+
+          echo "ARTIFACT_NAME=${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}_${{ matrix.cycamore_tag }}" >> "$GITHUB_ENV"
+
+      - name: Construct Artifact
+        if: github.event_name == 'pull_request'
+        run: |
+          echo "Build \`FROM cycamore_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cycamore:${{ matrix.cycamore_tag }}\` - ${{ env.BUILD_STATUS }}" > ${{ env.ARTIFACT_NAME }}.txt
+      
+      - name: Upload Artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ env.ARTIFACT_NAME }}
+          path: ${{ env.ARTIFACT_NAME }}.txt
+
+  upload-pr-number:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    steps:
+      - name: Save PR number to file
+        run: |
+          echo "${{ github.event.number }}" > pr_number
+      
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
         with:
-          comment_tag: ${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}_${{ matrix.cycamore_tag }}
-          message: |
-            ## Build statuses using cycamore_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}:${{ matrix.cycamore_tag }}
-            - Cymetric: ${{steps.build-cymetric.outcome == 'success' && '*Success* :white_check_mark:' || 
-                steps.build-cymetric.outcome == 'failure' && '**Failure** :x:' || 
-                '**Skipped due to upstream failure** :warning:'}}
+          name: pr_number
+          path: pr_number

.github/workflows/pr_comment.yml

@@ -0,0 +1,33 @@
+name: Comment on PR
+
+on:
+  workflow_run:
+    workflows: ["Build/Test for PR and collaborator push"]
+    types:
+      - completed
+
+jobs:
+  pr-comment:
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          run-id: ${{ github.event.workflow_run.id }}
+          merge-multiple: true
+
+      - name: Merge artifacts and get PR number
+        run: |
+          echo "### Build Status Report" > artifacts_merged.md
+          cat ./*.txt >> artifacts_merged.md
+          echo "PR_NUMBER=$(cat pr_number)" >> "$GITHUB_ENV"
+
+      - name: PR Comment
+        uses: thollander/actions-comment-pull-request@v2
+        with:
+          pr_number: ${{ env.PR_NUMBER }}
+          comment_tag: build_status_report
+          filePath: artifacts_merged.md
+

.github/workflows/publish_latest.yml

@@ -13,7 +13,10 @@ on:
 jobs:
   build-cymetric-and-push:
     runs-on: ubuntu-latest
-
+    permissions:
+      contents: read
+      packages: write
+
     strategy:
       matrix:
         ubuntu_versions : [
@@ -52,11 +55,11 @@ jobs:
       - name: Build and Test Cymetric
         uses: docker/build-push-action@v5
         with:
-          cache-from: type=registry,ref=ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache
-          cache-to: type=registry,ref=ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache,mode=max
+          cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache
+          cache-to: type=registry,ref=ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache,mode=max
           file: docker/Dockerfile
           push: true
-          tags: ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:${{ env.tag }}
+          tags: ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:${{ env.tag }}
           build-args: |
             pkg_mgr=${{ matrix.pkg_mgr }}
             ubuntu_version=${{ matrix.ubuntu_versions }}

.github/workflows/publish_release.yml

@@ -55,13 +55,13 @@ jobs:
       - name: Build and Test Cymetric
         uses: docker/build-push-action@v5
         with:
-          cache-from: type=registry,ref=ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache
-          cache-to: type=registry,ref=ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache,mode=max
+          cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache
+          cache-to: type=registry,ref=ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:ci-layer-cache,mode=max
           file: docker/Dockerfile
           push: true
           tags: |
-            ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:${{ env.version_tag }}
-            ghcr.io/cyclus/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:${{ env.stable_tag }}
+            ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:${{ env.version_tag }}
+            ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cymetric:${{ env.stable_tag }}
           build-args: |
             pkg_mgr=${{ matrix.pkg_mgr }}
             ubuntu_version=${{ matrix.ubuntu_versions }}

CHANGELOG.rst

@@ -4,10 +4,11 @@ cymetric Change Log
 
 .. current developments
 **Added:**
-* GitHub workflows for CI (#188, #190, #191, #192)
+* GitHub workflows for CI (#188, #190, #191, #192, #193)
 
 **Changed**
 * Converted test suite from nose to pytest (#188)
+* Removed some unused imports, mainly pyne (#184)
 
 v1.5.5
 ====================

README.rst

@@ -11,7 +11,7 @@ Dependencies
 First, please check to make sure you have all of the dependencies.
 
 Required dependencies:
-
+ 
 * Cyclus and its dependencies
 * `Jinja2 <http://jinja.pocoo.org/docs/dev/>`_
 * `pandas <http://pandas.pydata.org/>`_

cymetric/execution.py

@@ -13,6 +13,7 @@
 import numpy as np
 import pandas as pd
 
+
 from cymetric.evaluator import Evaluator, METRIC_REGISTRY
 
 

cymetric/fco_metrics.py

@@ -1,5 +1,7 @@
 """FCO metrics"""
 import pandas as pd
+
+
 try:
     from pyne import data
     import pyne.enrichment as enr
@@ -167,9 +169,15 @@ def fco_fuel_loading(mats, trans):
     mass = mass.groupby(mass.index)['Mass'].sum()
     mass = mass.reset_index()
     # sum by years (12 time steps)
-    mass = pd.DataFrame(data={'Year': mass.TimeCreated.apply(lambda x: x // 12),
-                              'FuelLoading': mass.Mass.apply(lambda x: x / 1000)},
-                        columns=['Year', 'FuelLoading'])
+    mass = pd.DataFrame(
+        data={
+            'Year': mass.TimeCreated.apply(
+                lambda x: x // 12),
+            'FuelLoading': mass.Mass.apply(
+                lambda x: x / 1000)},
+        columns=[
+            'Year',
+            'FuelLoading'])
     mass = mass.groupby('Year').sum()
     rtn = mass.reset_index()
     return rtn

cymetric/filters.py

@@ -1,6 +1,4 @@
 import warnings
-import pandas as pd
-import numpy as np
 
 try:
     from graphviz import Digraph
@@ -10,8 +8,6 @@
 
 try:
     from pyne import data
-    import pyne.enrichment as enr
-    from pyne import nucname
     HAVE_PYNE = True
 except ImportError:
     HAVE_PYNE = False

cymetric/graphs.py

@@ -2,23 +2,13 @@
 """
 import warnings
 
-import pandas as pd
-import numpy as np
 
 try:
     from graphviz import Digraph
     HAVE_GRAPHVIZ = True
 except ImportError:
     HAVE_GRAPHVIZ = False
 
-try:
-    from pyne import data
-    import pyne.enrichment as enr
-    from pyne import nucname
-    HAVE_PYNE = True
-except ImportError:
-    HAVE_PYNE = False
-
 from cymetric import tools
 from cymetric.filters import transactions_nuc
 

cymetric/metrics.py

@@ -6,9 +6,9 @@
 import numpy as np
 import pandas as pd
 
+
 try:
     from pyne import data
-    import pyne.enrichment as enr
     HAVE_PYNE = True
 except ImportError:
     HAVE_PYNE = False
@@ -284,7 +284,7 @@ def agents(entry, exit, decom, info):
     mergeon = ['SimId', 'AgentId']
     df = entry[['SimId', 'AgentId', 'Kind', 'Spec', 'Prototype', 'ParentId',
                 'Lifetime', 'EnterTime']]
-    df['ExitTime'] = [np.nan]*len(entry)
+    df['ExitTime'] = [np.nan] * len(entry)
     if exit is not None:
         exit.columns = ['SimId', 'AgentId', 'Exits']
         df = tools.merge_and_fillna_col(df, exit[['SimId', 'AgentId',

cymetric/schemas.py

@@ -8,7 +8,6 @@
 else:
     str_types = (str, unicode)
 
-from cyclus import typesystem as ts
 from cyclus.typesystem import NAMES, RANKS, IDS
 
 
@@ -40,8 +39,9 @@ def canon_shape(shape, dbtype):
             s.append(i)
         rank = RANKS[dbtype]
         if len(s) != rank:
-            msg = ('the shape rank for the {0} type must be {1}, got {2} for a '
-                   'shape of {3}.')
+            msg = (
+                'the shape rank for the {0} type must be {1}, got {2} for a '
+                'shape of {3}.')
             raise ValueError(msg.format(NAMES[dbtype], rank, len(s), s))
         rtn = tuple(s)
     elif isinstance(shape, int):

cymetric/timeseries.py

@@ -1,16 +1,5 @@
 import warnings
 
-import pandas as pd
-import numpy as np
-
-try:
-    from pyne import data
-    import pyne.enrichment as enr
-    from pyne import nucname
-    HAVE_PYNE = True
-except ImportError:
-    HAVE_PYNE = False
-
 from cymetric import tools
 from cymetric import filters
 
@@ -42,7 +31,12 @@ def transactions(evaler, senders=(), receivers=(), commodities=(), nucs=()):
     return df
 
 
-def transactions_activity(evaler, senders=(), receivers=(), commodities=(), nucs=()):
+def transactions_activity(
+        evaler,
+        senders=(),
+        receivers=(),
+        commodities=(),
+        nucs=()):
     """
     Shape the reduced transation Data Frame into a simple time serie. Applying nuclides selection when required.
 
@@ -86,8 +80,8 @@ def transactions_decayheat(
     if len(nucs) != 0:
         nucs = tools.format_nucs(nucs)
 
-    df = filters.transactions_decayheat(evaler, senders, receivers, commodities,
-                                        nucs)
+    df = filters.transactions_decayheat(
+        evaler, senders, receivers, commodities, nucs)
 
     df = df[['Time', 'DecayHeat']].groupby(['Time']).sum()
     df.reset_index(inplace=True)

cymetric/tools.py

@@ -5,12 +5,10 @@
 import sys
 import warnings
 
-import numpy as np
 import pandas as pd
 
+
 try:
-    from pyne import data
-    import pyne.enrichment as enr
     from pyne import nucname
     HAVE_PYNE = True
 except ImportError:
@@ -26,8 +24,9 @@ def dbopen(fname):
     """Opens a Cyclus database."""
     _, ext = os.path.splitext(fname)
     if ext not in EXT_BACKENDS:
-        msg = ('The backend database type of {0!r} could not be determined from '
-               'extension {1!r}.')
+        msg = (
+            'The backend database type of {0!r} could not be determined from '
+            'extension {1!r}.')
         raise ValueError(msg.format(fname, ext))
     db = EXT_BACKENDS[ext](fname)
     return db