Release v1.0.2

## Release (v1.0.2) Date 06.09.22 More thorough documentation, including updates to the paper. * PR #19 added coverage data and badges. * PR #20 created documentation for the notebooks to be used for the workshop. * PR #21 completed a draft of the paper for author comments period.
villano-lab · Jun 9, 2022 · d95c706 · d95c706
2 parents 7796aea + e63e43b
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diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,7 @@
+[run]
+branch = True
+[report]
+include = 
+    *.ipynb
+    *.py
+    python/*.py
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,18 +1,14 @@
 ## Template
-The following template is not required, but if you do not use it, please be sure to include all answers to all of the questions in some other way.
+The following template is not required, but if you do not use it, please include the following information in some other way.
 
 **Does your pull request resolve or partially resolve an issue?** 
-Yes / No.
+- [ ] Yes; it fully resolves #(issue number).
+- [ ] Yes; it partially resolves #(issue number).
+- [ ] No, it does not resolve an issue fully or partially.
 
-**If Yes, which issue?** 
-
-**Does your pull request implement code improvements?**
-Yes / No.
-
-**Does your pull request implement any breaking changes?**
-Yes / No.
-
-**If breaking changes are implemented, please describe:**
+**This pull request implements:**
+- [ ] Code improvements
+- [ ] Breaking changes (please describe any breaking changes below)
 
 **Testing:**  
 This pull request:

diff --git a/.github/workflows/draft-tex.yml b/.github/workflows/draft-tex.yml
@@ -18,7 +18,7 @@ jobs:
           args: paper/paper.md
         env:
           GIT_SHA: $GITHUB_SHA
-          JOURNAL: joss
+          JOURNAL: jose
       - uses: actions/upload-artifact@v2
         with:
           path: paper
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -18,7 +18,7 @@ build:
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/source/conf.py
-   fail_on_warning: false 
+   fail_on_warning: true 
 
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF

diff --git a/.travis.yml b/.travis.yml
@@ -21,7 +21,15 @@ install:
 
   - conda env create -n test-environment python=$TRAVIS_PYTHON_VERSION -f binder/environment.yml
   - source activate test-environment
+  #Packages for testing only -- don't need in user environment.
+  - pip3 install codecov pytest-cov pytest_notebook nbval papermill
+  - ipython kernel install --user --name=galactic-spin 
 
 before_script: cd binder
 script:
-- travis_wait 60 py.test
+- pytest --cov=./ --cov-report=xml --nbval --current-env --cov-config=../.coveragerc
+- papermill --prepare-only -p galaxy NGC5533 07_Bonus_Bulge_Rotation_Curve.ipynb 07_Bonus_Bulge_Rotation_Curve_NGC5533.ipynb
+- papermill --prepare-only -p galaxy NGC7814 07_Bonus_Bulge_Rotation_Curve.ipynb 07_Bonus_Bulge_Rotation_Curve_NGC7814.ipynb
+- pytest --cov=./ --cov-report=xml --nbval-lax 07_Bonus_Bulge_Rotation_Curve_NGC????.ipynb --cov-append --current-env --cov-config=../.coveragerc
+after_script:
+- codecov
diff --git a/README.md b/README.md
@@ -42,12 +42,14 @@ The three steps of the rotation curve building process is plotting the measured
 
 ## CITATION
 
-If you decide to use this code, or if you want to add a reference to it, please cite the latest archived version (soonTM),
+If you decide to use this code, or if you want to add a reference to it, please cite the latest archived version [at Zenodo](https://zenodo.org/record/6588351).
 
 ## VERSION HISTORY
 
-27.04.2022: Release of [version 1.0.0](https://github.com/villano-lab/galactic-spin-W1/releases/tag/v1.0.0)
+
+27.04.2022: Release of [version 1.0.2](https://github.com/villano-lab/galactic-spin-W1/releases/tag/v1.0.2)
 27.04.2022: Release of [version 1.0.1](https://github.com/villano-lab/galactic-spin-W1/releases/tag/v1.0.1)
+27.04.2022: Release of [version 1.0.0](https://github.com/villano-lab/galactic-spin-W1/releases/tag/v1.0.0)
 
 ## AUTHORS & CONTACT
 

diff --git a/RELEASENOTES.md b/RELEASENOTES.md
@@ -1,20 +1,25 @@
-## Future Release (v0.1.0) Date XX.XX.XX 
 
-* Many files were renamed to improve the organization of the repository.
-* Added Code of Conduct and Issue Templates.
-* PR #3 fixed with the provided environment that sometimes caused sliders not to update anything.
-* PR #4 added testing to Travis-CI
-* PR #? added documents such as CONTRIBUTING, PULL_REQUEST_TEMPLATE, and these RELEASENOTES.
+## Release (v1.0.2) Date 06.09.22
+
+More thorough documentation, including updates to the paper.
+* PR #19 added coverage data and badges.
+* PR #20 created documentation for the notebooks to be used for the workshop.
+* PR #21 completed a draft of the paper for author comments period.
 
 
-## Release (v0.0.1) Date 22.01.08 
+## Release (v1.0.1) Date 04.27.22 
 
-* Initial release! Repository created.
+* Merged branches to fix missing documentation updates.
 
 ## Release (v1.0.0) Date 04.27.22 
 
-* DM Workshop 1 released for RaCAS 2022.
+DM Workshop 1 released for RaCAS 2022.
+* Many files were renamed to improve the organization of the repository.
+* Added Code of Conduct and Issue Templates.
+* PR #3 fixed with the provided environment that sometimes caused sliders not to update anything.
+* PR #4 added testing to Travis-CI
+* PR #17 added documents such as CONTRIBUTING, PULL_REQUEST_TEMPLATE, and these RELEASENOTES.
 
-## Release (v1.0.1) Date 04.27.22 
+## Release (v0.0.1) Date 01.08.22
 
-* Merged branches.
+* Initial release! Repository created.
diff --git a/RELEASE_CHECKLIST.md b/RELEASE_CHECKLIST.md
@@ -8,11 +8,10 @@ Please be sure to do the following when making a release.
 5. Update release notes `RELEASENOTES.md`.
 6. Update `docs/source/index.rst` if badges changed.
 7. Restore fail-on-warning on .readthedocs.yaml if it was turned off.
-8. Make a release on github.
-9. Be sure the `stable` build of readthedocs points to the new release.
-10. Be sure to create a version on readthedocs of the new release. 
-11. If the version is a patch, deactivate the docs version for the previous patch of the same minor version. (Only one docs version for each minor version should be active at a time.)
-12. Be sure codecov website is switched to default to master branch.
-13. Update Zenodo.
-14. Move readthedocs latest to master branch.
-15. Remove items 14 and 15 from this list.
+8. Update all binder links in `docs/source/02_Modules.rst` to point to the upcoming version.
+9. Make a release on github.
+10. Be sure the `stable` build of readthedocs points to the new release.
+11. Be sure to create a version on readthedocs of the new release. 
+12. If the version is a patch, deactivate the docs version for the previous patch of the same minor version. (Only one docs version for each minor version should be active at a time.)
+13. Be sure codecov website is switched to default to master branch.
+14. Update Zenodo.
diff --git a/binder/01_DM_Rotation_Curve_Intro.ipynb b/binder/01_DM_Rotation_Curve_Intro.ipynb
@@ -375,6 +375,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the calculation time naturally varies.\n",
     "# Calculation time\n",
     "executionTime3 = (time.time() - startTime)\n",
     "ttt3=executionTime3/60\n",

diff --git a/binder/02_Widget_NGC5533_DMonly.ipynb b/binder/02_Widget_NGC5533_DMonly.ipynb
@@ -542,6 +542,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "# Widget\n",
     "VBox([button,out,interactive_plot(f)])"
    ]
@@ -603,7 +605,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/binder/03_Measured_Data_Plotting.ipynb b/binder/03_Measured_Data_Plotting.ipynb
@@ -250,6 +250,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the timing won't be exactly the same each time.\n",
     "# Time\n",
     "executionTime = (time.time() - startTime)\n",
     "ttt=executionTime/60\n",
@@ -295,7 +297,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/binder/04_Plotting_Rotation_Curves.ipynb b/binder/04_Plotting_Rotation_Curves.ipynb
diff --git a/binder/05_Widget_NGC5533_All_Components.ipynb b/binder/05_Widget_NGC5533_All_Components.ipynb
@@ -381,6 +381,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the figure doesn't save to the repository correctly.\n",
     "# Widget\n",
     "VBox([button,out,interactive_plot(f)])"
    ]
@@ -446,7 +448,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/binder/06_Plotting_SPARC_data.ipynb b/binder/06_Plotting_SPARC_data.ipynb
diff --git a/binder/07_Bonus_Bulge_Rotation_Curve.ipynb b/binder/07_Bonus_Bulge_Rotation_Curve.ipynb
@@ -60,7 +60,11 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
    "outputs": [],
    "source": [
     "galaxy = \"NGC891\"         # Change this value to select a galaxy out of the 3 choices: NGC5533, NGC891, NGC7814"
@@ -105,6 +109,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the filepath won't be the same across devices\n",
     "import importlib\n",
     "importlib.reload(b)             # Reload library so the changes take effect"
    ]
@@ -635,6 +641,8 @@
     }
    ],
    "source": [
+    "#NBVAL_IGNORE_OUTPUT\n",
+    "#Because the timing won't be exactly the same each time.\n",
     "executionTime = (time.time() - startTime)\n",
     "print(f'Execution time: {executionTime:.2f} seconds')"
    ]
@@ -682,9 +690,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "galactic-spin",
    "language": "python",
-   "name": "python3"
+   "name": "galactic-spin"
   },
   "language_info": {
    "codemirror_mode": {
@@ -696,7 +704,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/binder/08_Interactive_Fitting.ipynb b/binder/08_Interactive_Fitting.ipynb