Deploy testing (#114)

* split up workflows to make checks easier

* bump verson for testing

* building workflow dependencies

* homogenizing some of the workflows

* bump version number, add missing doi

* another doi

* update cif to match zenodo.  typo in affiliations

* some mistakes in workflows

* working out inheritance

* try without forwarding

* trying to include token

* old api for tesst pypi

* typo

* disable other tests for now

* trying to get the right files

* try to find the artefact

* bumping version

* moveing dir

* some cleanup. separating and Upgrading test.pypi

* bump versions

* actions finally working, cleaning up, bump version

* bumping version for release

* update cif file

* bump version for pypi

* another version bump

.github/workflows/pypackage.yml

@@ -0,0 +1,39 @@
+name: Build Wheel
+on: [workflow_call]
+
+jobs:
+  build-wheel:
+    name: Build Wheel for Testing
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+      - name: install check-wheel-contents
+        run: >-
+          python3 -m
+          pip install
+          check-wheel-contents
+      - name: check wheel
+        run: >-
+          check-wheel-contents
+          dist/*.whl
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./dist/*
+

.github/workflows/pypublish.yml

@@ -1,60 +1,45 @@
 name: Publish Python distribution to PyPI and TestPyPI
-on: push
+on:
+  push:
+    tags:
+      - '*'
 
 jobs:
   build-wheel:
-    name: build wheel for testing
+    uses: ./.github/workflows/pypackage.yml
+  upload_testpypi:
+    name: Publish build to TestPyPI
+    needs: [build-wheel]
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://test.pypi.org/p/UncertainSCI
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v3
+      - uses: actions/download-artifact@v3
         with:
-          python-version: 3.9
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-      - name: install check-wheel-contents
-        run: >-
-          python3 -m
-          pip install
-          check-wheel-contents
-      - name: check wheel
-        run: >-
-          check-wheel-contents
-          dist/*.whl
-      - uses: actions/upload-artifact@v3
+          name: artifact
+          path: dist
+      - name: Upload to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          path: ./dist/*
-
+          packages-dir: dist
   upload_pypi:
-    needs: build-wheel
-    name: Publish build to TestPyPI and PyPI
+    name: Publish build to PyPI
+    needs: [build-wheel, upload_testpypi]
     runs-on: ubuntu-latest
     environment:
       name: pypi
       url: https://pypi.org/p/UncertainSCI
     permissions:
       id-token: write
-    if: startsWith(github.event.ref, 'refs/tags')
     steps:
       - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
-      - name: Upload to TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository_url: https://test.pypi.org/legacy/
       - name: Upload to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist

.github/workflows/pythonapp.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Build
 
 on: [push, pull_request]

.github/workflows/testpackage.yml

@@ -0,0 +1,6 @@
+name: Build and Test Package
+on: [push, pull_request]
+
+jobs:
+  buildwheel:
+    uses: ./.github/workflows/pypackage.yml

CITATION.cff

@@ -1,4 +1,4 @@
-cff-version: 1.0
+cff-version: 1.1.0
 message: "If you use this software, please cite it as below."
 authors:
   - family-names: Tate
@@ -31,6 +31,6 @@ authors:
   - family-names: Narayan
     given-names: Akil
     orcid: https://orcid.org/0000-0002-5914-4207
-title: SCIInstitute/UncertainSCI: v1.0
-version: v1.0
-date-released: 2023-08-08
+title: UncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelines
+version: v1.0.1
+date-released: 2023-10-11

paper/paper.bib

@@ -149,6 +149,7 @@ @Article{JDT:Xu2014
   pages =        "529--537",
   title =        "Variational Bayesian electrophysiological imaging of
                  myocardial infarction.",
+  doi = "10.1007/978-3-319-10470-6_66",             
   volume =       "17",
   year =         "2014",
 }	
@@ -159,6 +160,7 @@ @book{ACN:Xiu2010
 	shorttitle = {Numerical {Methods} for {Stochastic} {Computations}},
 	publisher = {Princeton University Press},
 	author = {Xiu, D.},
+	doi = {10.1007/978-3-319-10470-6_66}, 
 	month = jul,
 	year = {2010}
 }

paper/paper.md

@@ -32,7 +32,7 @@ authors:
     affiliation: 6
   - name: Rob S MacLeod
     orcid: 0000-0002-0000-0356
-    affiliation: "1, 3"
+    affiliation: "1, 3, 4"
   - name: Akil Narayan
     orcid: 0000-0002-5914-4207
     affiliation: "1, 2"

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='UncertainSCI',
-    version='1.0.1',
+    version='1.0.1.1',
     author='UncertainSCI Developers',
     author_email='[email protected]',
     packages=find_packages(),