docs: env file fix and pull request templates (#170)

.github/PULL_REQUEST_TEMPLATE

@@ -0,0 +1,75 @@
+# Espresso Pull Request Template
+
+## Description
+
+Please provide a clear and concise description of the changes you've made.
+
+If you are adding a new `EspressoProblem`, read the 
+[Contributor's Guide](https://geo-espresso.readthedocs.io/en/latest/contributor_guide/index.html) 
+as a reference. Otherwise refer to the 
+[Developer's Guide](https://geo-espresso.readthedocs.io/en/latest/developer_guide/develop.html).
+
+## Type of Change
+
+Please indicate the type of change this pull request represents:
+
+- [ ] New Espresso problem or example
+- [ ] Espresso core
+- [ ] Espresso machine
+- [ ] Documentation
+- [ ] Others (please specify here)
+
+## Checklist for new `EspressoProblem` (remove me if not applicable)
+
+### Requirements
+
+Please list any requirements or dependencies for running the problem here.
+
+### Additional information
+
+Provide any additional information on how to run the problem or context about it here.
+
+### Jupyter Notebook
+
+If applicable, provide a brief description of the Jupyter notebook included with this problem.
+
+### Testing
+
+To validate your problem:
+
+```console
+$ python espresso_machine/build_package/build.py --pre --post -c <example_name>
+```
+
+Please confirm that you have tested your problem:
+
+- [ ] I have checked that all tests pass locally with my changes
+- [ ] I have ensured that my code follows the style guidelines of this project
+
+### Licence
+
+Confirm the licence under which this problem is distributed.
+
+## Checklist for Espresso core (remove me if not applicable)
+
+- [ ] My changes are backward compatible
+- [ ] The new contribution generation script is compatible with the new changes
+- [ ] The build script is compatible with the new changes
+- [ ] The validation script is compatible with the new changes
+- [ ] The documentation is up to date with the new changes
+- [ ] I have formatted the Python files with `black`
+
+## Checklist for Espresso machine (remove me if not applicable)
+
+- [ ] My changes are backward compatible
+- [ ] The documentation is up to date with the new changes
+- [ ] I have formatted the Python files with `black`
+
+## Checklist for Espresso documentation (remove me if not applicable)
+
+- [ ] I have built the documentation by running `make html` in the `docs/` folder
+- [ ] I have served the website locally by running `python -m http.server 8000 -d build/html` and checked the changes at `localhost:8000`
+
+## Additional Information
+
+Please provide any additional information or context about the pull request here.

.github/workflows/pr_validation.yml

@@ -54,10 +54,14 @@ jobs:
  run: |
  if [[ -f "changed_contribs.txt" ]]
  then
+ echo "Tests will be run on the following contributions:"
  cat changed_contribs.txt
  python espresso_machine/build_package/build.py -f changed_contribs.txt --no-install
  pip install -v _esp_build/
- python espresso_machine/build_package/test_examples.py -f changed_contribs.txt --post
+ python espresso_machine/build_package/test_examples.py -f changed_contribs.txt
  else
- python espresso_machine/build_package/build.py --post
+ echo "Tests will be run on the entire package."
+ python espresso_machine/build_package/build.py --no-install
+ pip install -v _esp_build/
+ python espresso_machine/build_package/test_examples.py
  fi

docs/environment.yml

@@ -2,7 +2,7 @@ name: readthedocs
 dependencies:
  - python=3.10
  - matplotlib>=3.5.0
- - scipy>=1.0.0
+ - scipy<1.13.0 # TODO remove this after seislib releases new version
  - cython
  - obspy
  - cartopy

docs/source/conf.py

@@ -44,7 +44,7 @@ def setup(app):
 project = 'Espresso'
 copyright = f"{datetime.date.today().year}, InLab, {project} development team"
 _version_short = esp.__version__.split("+")[0]
-version = "dev" if "dev" in esp.__version__ else _version_short
+version = "dev" if "dev" in esp.__version__ else f"v{_version_short}"
 
 
 # -- General configuration ---------------------------------------------------

docs/source/index.rst

@@ -32,13 +32,6 @@ Welcome to Espresso!
  developer_guide/index.rst
 
 
-.. .. toctree::
-.. :hidden:
- 
-.. GitHub repository <https://github.com/inlab-geo/espresso/>
-.. Issue tracker <https://github.com/inlab-geo/espresso/issues/>
-
-
 You've just come up with a new optimisation algorithm, inversion strategy, or machine learning-based inference framework. Now you want to see how it performs on a real-world problem... 
 
 Espresso (**E**\ arth **s**\ cience **pr**\ oblems for the **e**\ valuation of **s**\ trategies, **s**\ olvers and **o**\ ptimizers) aims to make this as easy as possible. It provides access to a range of exemplars via a standardized Python interface, including domain-expert--curated datasets and corresponding simulation codes. Swapping from one test problem to the next is just one line of code.
@@ -143,4 +136,4 @@ If this looks interesting, you can:
  Accept this invitation to join the conversation on Slack
 
 
-Espresso is an open-source community effort, currently supported and coordinated by `InLab <http:https://www.inlab.edu.au/>`_.
+Espresso is an open-source community effort, currently supported and coordinated by `InLab <https:https://inlab.au>`_.