Ci/change release trigger (#29)

* Fix bot aliases in .mailmap (tardis-sn#2038) * Added v_inner and v_outer, enable_nonhomologous_expansion for future use in nonhomologous expansion (tardis-sn#2024) * added v_outer and v_inner to NumbaModel * defined default value for v_inner and v_outer in NumbaModel * added enable_nonhomologous_expansion to io/schemas/montecarlo.yml * added v_inner and v_outer to NumbaPlasma * added v_inner and v_outer as arguments for NumbaModel in run() in montecarlo_numba * added v_outer_cgs to MonteCarloRunner * removed a comment * ran black on the changed files * added right arguments in test * added v_inner, v_outer to tests * added temporary fix to formal_integral.py * ran black on modified files * changed dummy values in the test * Reverted content of file. * made needed change in test_cuda_formal_integral.py * made needed change in test_numba_formal_integral.py * Update README.rst in post-release (tardis-sn#2037) * Fix docs badge * Add license badge * First attempt of creating credits.rst and README.rst via templates * Working version * Restore old README.rst * Update post-release workflow * Change .gitignore * Various fixes * Check PEP8 on CI (tardis-sn#2039) * Add Flake8 job * Change to file description * Test payload Co-authored-by: Sona Chitchyan <[email protected]>
epassaro · Jun 2, 2022 · 2a15557 · 2a15557
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diff --git a/.ci-helpers/update_credits.py b/.ci-helpers/update_credits.py
@@ -0,0 +1,77 @@
+"""Script for updating `credits.rst` and `README.rst` between releases,
+requires the `rst-include` package"""
+
+import pathlib
+import re
+import textwrap
+import warnings
+
+import requests
+from rst_include import rst_include
+
+
+def generate_zenodo():
+    """Generates `zenodo.rst` file with BibTeX citation
+    Adapted from: https://astrodata.nyc/posts/2021-04-23-zenodo-sphinx/"""
+
+    CONCEPT_DOI = "592480"  # See: https://help.zenodo.org/#versioning
+    zenodo_path = pathlib.Path("docs/resources/zenodo.rst")
+
+    try:
+        headers = {"accept": "application/x-bibtex"}
+        response = requests.get(
+            f"https://zenodo.org/api/records/{CONCEPT_DOI}", headers=headers
+        )
+        response.encoding = "utf-8"
+        citation = re.findall("@software{(.*)\,", response.text)
+        zenodo_record = (
+            f".. |ZENODO| replace:: {citation[0]}\n\n"
+            ".. code-block:: bibtex\n\n"
+            + textwrap.indent(response.text, " " * 4)
+        )
+
+    except Exception as e:
+        warnings.warn(
+            "Failed to retrieve Zenodo record for TARDIS: " f"{str(e)}"
+        )
+
+        not_found_msg = """
+                        Couldn"t retrieve the TARDIS software citation from Zenodo. Get it 
+                        directly from `this link <https://zenodo.org/record/{CONCEPT_DOI}>`_    .
+                        """
+
+        zenodo_record = (
+            ".. |ZENODO| replace:: <TARDIS SOFTWARE CITATION HERE> \n\n"
+            ".. warning:: \n\n" + textwrap.indent(not_found_msg, " " * 4)
+        )
+
+    with open(zenodo_path, "w") as f:
+        f.write(zenodo_record)
+
+    print(zenodo_record)
+
+
+def main():
+    generate_zenodo()
+
+    rst_include.include(
+        source="docs/resources/credits_template.rst",
+        target="docs/resources/credits.rst",
+        quiet=False,
+        inplace=False,
+        source_encoding="utf-8",
+        target_encoding="utf-8",
+    )
+
+    rst_include.include(
+        source="README_TEMPLATE.rst",
+        target="README.rst",
+        quiet=False,
+        inplace=False,
+        source_encoding="utf-8",
+        target_encoding="utf-8",
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
diff --git a/.github/workflows/codestyle.yml b/.github/workflows/codestyle.yml
@@ -0,0 +1,48 @@
+#  For more information about TARDIS pipelines, please refer to:
+#
+#    https://tardis-sn.github.io/tardis/development/continuous_integration.html
+
+name: codestyle
+
+on:
+  push:
+    branches:
+    - '*'
+
+  pull_request:
+    branches:
+    - '*'
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+
+      - name: Install Black
+        run: pip install black==22.3
+
+      - name: Run Black
+        run: black --check tardis
+
+  flake8:
+    if: false
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+
+      - name: Install Flake8
+        run: pip install flake8==4.0.1 pep8-naming==0.12.1
+
+      - name: Run Flake8
+        run: flake8 tardis
diff --git a/.github/workflows/payload.yml b/.github/workflows/payload.yml
@@ -0,0 +1,13 @@
+name: payload
+
+on:
+  push:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo $PAYLOAD
+        env:
+          PAYLOAD: ${{ github.event }}
diff --git a/.github/workflows/post-release.yml b/.github/workflows/post-release.yml
@@ -37,7 +37,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Wait for Zenodo webhook
-        run: sleep 120
+        run: sleep 180
 
       - name: Setup Python
         uses: actions/setup-python@v3
@@ -57,6 +57,32 @@ jobs:
           name: citation
           path: CITATION.cff
 
+  credits:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Wait for Zenodo webhook
+        run: sleep 180
+
+      - name: Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+
+      - name: Install rst-include 
+        run: pip install rst-include requests
+
+      - name: Update README.rst
+        run: python .ci-helpers/update_credits.py
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: credits
+          path: |
+            README.rst
+            docs/resources/credits.rst
+
   pull_request:
     needs: [changelog, citation]
     runs-on: ubuntu-latest
@@ -71,6 +97,7 @@ jobs:
         run: |
           cp /tmp/changelog/CHANGELOG.md .
           cp /tmp/citation/CITATION.cff .
+          cp -r /tmp/credits/* .
 
       - name: Get current date
         run: echo "DATE=$(date +'%Y.%m.%d')" >> $GITHUB_ENV

diff --git a/.gitignore b/.gitignore
@@ -25,7 +25,6 @@ MANIFEST
 # Sphinx
 docs/api
 docs/_build
-docs/resources/ZENODO.rst
 docs/tutorials.rst
 docs/io/configuration/components/models/converters/density_parse.csv
 docs/io/configuration/components/models/converters/abund_parse.csv

diff --git a/.mailmap b/.mailmap
@@ -172,10 +172,11 @@ Stuart Sim <[email protected]> ssim <[email protected]>
 Stuart Sim <[email protected]> Stuart Sim <[email protected]>
 Stuart Sim <[email protected]> Stuart Sim <[email protected]>
 
-tardis-bot <[email protected]>
-tardis-bot <[email protected]> tardis-bot <[email protected]>
-tardis-bot <[email protected]> tardis-bot <[email protected]>
-tardis-bot <[email protected]> tardis-bot <[email protected]>
+TARDIS Bot <[email protected]>
+TARDIS Bot <[email protected]> tardis-bot <[email protected]>
+TARDIS Bot <[email protected]> TARDIS Bot <[email protected]>
+TARDIS Bot <[email protected]> TARDIS Bot <[email protected]>
+TARDIS Bot <[email protected]> Azure Pipelines <[email protected]>
 
 Tomas Bylund <[email protected]>
 Tomas Bylund <[email protected]> Tobychev <[email protected]>

diff --git a/README_TEMPLATE.rst b/README_TEMPLATE.rst
@@ -0,0 +1,56 @@
+======
+TARDIS
+======
+
+.. image:: https://img.shields.io/badge/Donate-to%20TARDIS-brightgreen.svg
+    :target: https://numfocus.salsalabs.org/donate-to-tardis/index.html
+
+.. image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
+    :target: http://numfocus.org
+
+.. image:: https://badges.gitter.im/Join%20Chat.svg
+    :target: https://gitter.im/tardis-sn/tardis
+
+.. image:: https://img.shields.io/static/v1?logo=visualstudiocode&label=&message=Open%20in%20Visual%20Studio%20Code&labelColor=2c2c32&color=007acc&logoColor=007acc
+    :target: https://open.vscode.dev/tardis-sn/tardis
+|
+
+TARDIS is a tool that creates synthetic observations (*spectra*) for exploding
+stars (*supernovae*).
+
+.. image:: https://codecov.io/gh/tardis-sn/tardis/branch/master/graph/badge.svg
+    :target: https://codecov.io/gh/tardis-sn/tardis
+
+.. image:: https://img.shields.io/endpoint?url=https://jsonbin.org/tardis-bot/tardis/badges/docstr-cov
+    :target: https://github.com/tardis-sn/tardis/actions/workflows/docstr-cov.yml?query=branch%3Amaster
+
+.. image:: https://github.com/tardis-sn/tardis/actions/workflows/tests.yml/badge.svg
+    :target: https://github.com/tardis-sn/tardis/actions/workflows/tests.yml
+
+.. image:: https://github.com/tardis-sn/tardis/actions/workflows/build-docs.yml/badge.svg
+    :target: https://tardis-sn.github.io/tardis/index.html
+
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :target: https://github.com/psf/black
+|
+
+
+.. include:: docs/resources/credits.rst
+
+
+*******
+License
+*******
+
+.. image:: https://img.shields.io/conda/l/conda-forge/tardis-sn
+    :target: https://github.com/tardis-sn/tardis/blob/master/licenses/LICENSE.rst
+
+.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
+    :target: http://www.astropy.org
+|
+
+This project is Copyright (c) TARDIS Collaboration and licensed under
+the terms of the BSD 3-Clause license. This package is based upon
+the `Astropy package template <https://github.com/astropy/package-template>`_
+which is licensed under the BSD 3-clause license. See the licenses folder for
+more information.
diff --git a/docs/conf.py b/docs/conf.py
@@ -63,6 +63,7 @@
 # directories to ignore when looking for source files.
 exclude_patterns.append("_templates")
 exclude_patterns.append("_build")
+exclude_patterns.append("**_template.rst")
 exclude_patterns.append("**.ipynb_checkpoints")
 exclude_patterns.append("resources/research_done_using_TARDIS/ads.ipynb")
 
@@ -334,54 +335,8 @@
 
 # -- Sphinx hook-ins ---------------------------------------------------------
 
-import re
-import pathlib
-import requests
-import textwrap
-import warnings
 from shutil import copyfile
 
-
-def generate_ZENODO(app):
-    """Creating ZENODO.rst
-    Adapted from: https://astrodata.nyc/posts/2021-04-23-zenodo-sphinx/"""
-    CONCEPT_DOI = "592480"  # See: https://help.zenodo.org/#versioning
-    zenodo_path = pathlib.Path("resources/ZENODO.rst")
-
-    try:
-        headers = {"accept": "application/x-bibtex"}
-        response = requests.get(
-            f"https://zenodo.org/api/records/{CONCEPT_DOI}", headers=headers
-        )
-        response.encoding = "utf-8"
-        citation = re.findall("@software{(.*)\,", response.text)
-        zenodo_record = (
-            f".. |ZENODO| replace:: {citation[0]}\n\n"
-            ".. code-block:: bibtex\n\n"
-            + textwrap.indent(response.text, " " * 4)
-        )
-
-    except Exception as e:
-        warnings.warn(
-            "Failed to retrieve Zenodo record for TARDIS: " f"{str(e)}"
-        )
-
-        not_found_msg = """
-                        Couldn"t retrieve the TARDIS software citation from Zenodo. Get it 
-                        directly from `this link <https://zenodo.org/record/{CONCEPT_DOI}>`_    .
-                        """
-
-        zenodo_record = (
-            ".. |ZENODO| replace:: <TARDIS SOFTWARE CITATION HERE> \n\n"
-            ".. warning:: \n\n" + textwrap.indent(not_found_msg, " " * 4)
-        )
-
-    with open(zenodo_path, "w") as f:
-        f.write(zenodo_record)
-
-    print(zenodo_record)
-
-
 def generate_tutorials_page(app):
     """Create tutorials.rst"""
     notebooks = ""
@@ -434,7 +389,6 @@ def create_redirect_files(app, docname):
 
 
 def setup(app):
-    app.connect("builder-inited", generate_ZENODO)
     app.connect("builder-inited", generate_tutorials_page)
     app.connect("autodoc-skip-member", autodoc_skip_member)
     app.connect("build-finished", create_redirect_files)
diff --git a/docs/resources/credits.rst → docs/resources/credits_template.rst b/docs/resources/credits.rst → docs/resources/credits_template.rst
@@ -72,4 +72,4 @@ The following BibTeX entries are needed for the references:
           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
-.. include:: ZENODO.rst
+.. include:: zenodo.rst
diff --git a/tardis/io/schemas/montecarlo.yml b/tardis/io/schemas/montecarlo.yml
@@ -64,6 +64,10 @@ properties:
     default: false
     description: Enables a more complete treatment of relativitic effects. This includes
       angle aberration as well as use of the fully general Doppler formula.
+  enable_nonhomologous_expansion:
+    type: boolean
+    default: false
+    description: Enables nonhomologous expansion. Treats shells as piece-wise homologous areas for velocity-radius dependence.
   tracking:
     type: object
     default: {}

diff --git a/tardis/montecarlo/base.py b/tardis/montecarlo/base.py
@@ -202,6 +202,7 @@ def _initialize_geometry_arrays(self, model):
         self.r_inner_cgs = model.r_inner.to("cm").value
         self.r_outer_cgs = model.r_outer.to("cm").value
         self.v_inner_cgs = model.v_inner.to("cm/s").value
+        self.v_outer_cgs = model.v_outer.to("cm/s").value
 
     def _initialize_packets(self, T, no_of_packets, iteration, radius):
         # the iteration is added each time to preserve randomness