Merge pull request #188 from cyclus/convert-ci

Update Cymetric CI

.github/workflows/build_test.yml

@@ -0,0 +1,63 @@
+name: Build/Test for PR and collaborator push
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  pull_request:
+    paths-ignore:
+      - '.github/workflows/build_test_publish.yml'
+      - 'docker/**'
+      - 'doc/**'
+      - 'CHANGELOG.rst'
+  push:
+    paths-ignore:
+      - '.github/workflows/build_test_publish.yml'
+      - 'docker/**'
+      - 'doc/**'
+      - 'CHANGELOG.rst'
+
+jobs:
+  build-and-test:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        ubuntu_versions : [
+          20.04,
+          22.04,
+        ]
+        pkg_mgr : [
+          apt,
+          conda,
+        ]
+        cycamore_tag: [
+          latest,
+        ]
+
+    container:
+      image: ghcr.io/cyclus/cycamore_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}/cycamore:${{matrix.cycamore_tag}}
+
+    steps:
+      - name: Checkout Cymetric
+        uses: actions/checkout@v3
+
+      - name: Install Cymetric Apt Dependencies
+        if: matrix.pkg_mgr == 'apt'
+        run: |
+          apt update --fix-missing && apt install -y python3-pip python3-pytest
+      
+      - name: Install Cymetric Conda Dependencies
+        if: matrix.pkg_mgr == 'conda'
+        run: |
+          mamba install -y pip pytest
+
+      - name: Build Cymetric
+        run: |
+          python -m pip install --target $(python -m site --user-site) .
+
+      - name: Cymetric Tests
+        run: |
+          export PYTHONPATH=$(find /root/.local/lib -type d -name 'cyclus-*-*.egg' -print -quit)
+          cd tests && python -m pytest

.github/workflows/build_test_publish.yml

@@ -0,0 +1,60 @@
+name: Build and Publish Cymetric Images
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - '.github/workflows/build_test_publish.yml'
+      - 'docker/**'
+  push:
+    branches:
+      - main
+
+jobs:
+  build-dependency-and-test-img:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        ubuntu_versions : [
+          20.04,
+          22.04,
+        ]
+        pkg_mgr : [
+          apt,
+          conda,
+        ]
+
+    name: Installing Dependencies, Building Cymetric and Running Tests
+    steps:
+      - name: default environment
+        run: |
+          echo "tag-latest-on-default=false" >> "$GITHUB_ENV"
+
+      - name: condition on trigger parameters
+        if: ${{ github.repository_owner == 'cyclus' && github.ref == 'refs/heads/main' }}
+        run: |
+          echo "tag-latest-on-default=true" >> "$GITHUB_ENV"
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Multi-Stage Build Action
+        uses: firehed/multistage-docker-build-action@v1
+        with:
+          repository: ghcr.io/${{ github.repository_owner }}/cymetric_${{ matrix.ubuntu_versions }}_${{ matrix.pkg_mgr }}
+          stages: cymetric
+          server-stage: cymetric-pytest
+          quiet: false
+          parallel: true
+          tag-latest-on-default: ${{ env.tag-latest-on-default }}
+          dockerfile: docker/Dockerfile
+          build-args: pkg_mgr=${{ matrix.pkg_mgr }}, ubuntu_version=${{ matrix.ubuntu_versions }}

.github/workflows/changelog_test.yml

@@ -0,0 +1,37 @@
+name: Changelog check
+
+on:
+  # allows us to run workflows manually
+  workflow_dispatch:
+  pull_request:
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  changelog_update:
+    runs-on: ubuntu-latest
+    container:
+      image: alpine:3.14
+
+    name: Is Changelog up-to-date ?
+    steps:
+      - name: Install latest git
+        run: |
+          apk add --no-cache bash git openssh
+          git --version
+
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - run: |
+          git config --global --add safe.directory ${GITHUB_WORKSPACE}
+          cd $GITHUB_WORKSPACE
+          git remote add cymetric https://github.com/cyclus/cymetric.git
+          git fetch cymetric
+          change=`git diff cymetric/main -- CHANGELOG.rst | wc -l`
+          git remote remove cymetric
+          if [ $change -eq 0 ]; then 
+            echo "CHANGELOG.rst has not been updated"
+            exit 1 
+          fi

CHANGELOG.rst

@@ -3,6 +3,12 @@ cymetric Change Log
 ===================
 
 .. current developments
+**Added:**
+* GitHub workflows for CI (#188)
+
+**Changed**
+* Converted test suite from nose to pytest (#188)
+
 v1.5.5
 ====================
 

README.rst

@@ -40,13 +40,13 @@ Then build and install to the same location Cyclus is installed:
 .. code-block:: bash
 
     $ cd cymetric
-    $ python setup.py install --prefix $(cyclus --install-path)
+    $ python -m pip install --target $(python -m site --user-site)
 
 Next, run the tests to ensure everything is working properly:
 
 .. code-block:: bash
 
-    $ nosetests -w tests/
+    $ python -m pytest tests/
 
 Installation via Binary
 ~~~~~~~~~~~~~~~~~~~~~~~

cymetric/execution.py

@@ -4,7 +4,7 @@
 import re
 import sys
 import uuid
-from collections import MutableMapping, Sized
+from collections.abc import MutableMapping, Sized
 if sys.version_info[0] > 2:
     str_types = (str, bytes)
 else:

cymetric/metrics.py

@@ -153,7 +153,7 @@ def activity(mats):
                                 'TimeCreated', 'NucId'),
                                'Mass')
     act = []
-    for (simid, qual, res, obj, time, nuc), m in mass.iteritems():
+    for (simid, qual, res, obj, time, nuc), m in mass.items():
         val = (1000 * data.N_A * m * data.decay_const(nuc)
                / data.atomic_mass(nuc))
         act.append(val)
@@ -192,7 +192,7 @@ def decay_heat(acts):
                                'TimeCreated', 'NucId'),
                               'Activity')
     dh = []
-    for (simid, qual, res, obj, time, nuc), a in act.iteritems():
+    for (simid, qual, res, obj, time, nuc), a in act.items():
         val = (data.MeV_per_MJ * a * data.q_val(nuc))
         dh.append(val)
     dh = pd.Series(dh, index=act.index)
@@ -530,7 +530,7 @@ def timelist(info):
     """
     info = tools.raw_to_series(info, ('SimId',), 'Duration')
     tl = []
-    for sim, dur in info.iteritems():
+    for sim, dur in info.items():
         for i in range(dur):
             tl.append((sim, i))
     tl = pd.DataFrame(tl, columns=['SimId', 'TimeStep'])

cymetric/schemas.py

@@ -2,7 +2,7 @@
 """
 from __future__ import print_function, unicode_literals
 import sys
-from collections import MutableSequence, Iterable
+from collections.abc import MutableSequence, Iterable
 if sys.version_info[0] > 2:
     str_types = (str, bytes)
 else:

cymetric/tools.py

@@ -109,7 +109,7 @@ def add_missing_time_step(df, ref_time):
     ref_time.rename(index=str, columns={'TimeStep': 'Time'}, inplace=True)
 
     if 'SimId' in ref_time.columns.values:
-        ref_time.drop('SimId', 1, inplace=True)
+        ref_time.drop('SimId', axis=1, inplace=True)
     df = pd.merge(ref_time, df, how="outer")
     df.fillna(0, inplace=True)
     return df
@@ -129,7 +129,7 @@ def merge(df, base_col, add_df, add_col):
     add_col: columns to be added
     """
     df = pd.merge(add_df[add_col], df, on=base_col)
-    df.drop(base_col[1], 1)
+    df.drop(base_col[1], axis=1)
     return df
 
 

docker/Dockerfile

@@ -0,0 +1,18 @@
+ARG pkg_mgr=apt
+ARG ubuntu_version=22.04
+
+FROM ghcr.io/cyclus/cycamore_${ubuntu_version}_${pkg_mgr}/cycamore as cycamore
+
+FROM cycamore as apt-deps
+RUN apt update --fix-missing && apt install -y python3-pip python3-pytest
+
+FROM cycamore as conda-deps
+RUN mamba install -y pip pytest
+
+FROM ${pkg_mgr}-deps as cymetric
+COPY . /cymetric
+WORKDIR /cymetric
+RUN python -m pip install --target $(python -m site --user-site) .
+
+FROM cymetric as cymetric-pytest
+RUN cd tests && python -m pytest