Dev

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing
+# How to contribute
 
 See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
 description of best practices for developing scientific packages.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,27 @@
+---
+name: Bug report
+about: Report a problem/bug to help us improve.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Full code that generate the error**
+<!--
+Include any data files or inputs required to run the code. It really helps if
+we can run the code on our own machines.
+-->
+
+```python
+PASTE YOUR CODE HERE
+```
+
+**Full error message**
+
+```
+PASTE ERROR MESSAGE HERE
+```

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,22 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Description of the desired feature:**
+
+<!--
+Add as much detail as you can in your description below. If possible, include an
+example of how you would like to use this feature (even better if it's a code
+example).
+-->
+
+**Are you willing to help implement and maintain this feature?**
+
+<!--
+Every feature we add is code that we will have to maintain and keep updated.
+Please let us know if you're willing to help maintain this feature in the future.
+-->

.github/config.yml

@@ -0,0 +1,24 @@
+# Inspired by [PyGMT](https://github.com/GenericMappingTools/pygmt) welcome messages.
+# Configuration for welcome - https://github.com/behaviorbot/welcome
+
+# Configuration for new-issue-welcome - https://github.com/behaviorbot/new-issue-welcome
+
+# Comment to be posted to on first time issues
+newIssueWelcomeComment: >
+  👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our [contributing guidelines](https://github.com/mdtanker/invert4geom/blob/main/docs/contribute.md).
+# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  💖 Thanks for opening this pull request! 💖
+  Please make sure you read our [contributing guidelines](https://github.com/mdtanker/invert4geom/blob/main/.github/CONTRIBUTING.md).
+  A few things to keep in mind:
+  * If you need help writing tests, take a look at the existing ones for inspiration. If you don't know where to start, let us know and we'll walk you through it.
+  * All new features should be documented. It helps to write the docstrings for your functions/classes before writing the code. This will help you think about your code design and results in better code.
+  * No matter what, we are really grateful that you put in the effort to do this! 🎉
+# Configuration for first-pr-merge - https://github.com/behaviorbot/first-pr-merge
+
+# Comment to be posted to on pull requests merged by a first time user
+firstPRMergeComment: >
+   🎉🎉🎉 Congrats on merging your first pull request and welcome to the team! 🎉🎉🎉
+   We hope that this was a good experience for you. Let us know if there is any way that the contributing process could be improved.

.pre-commit-config.yaml

@@ -14,6 +14,9 @@ exclude: |
       docs/api/invert4geom.regional.rst|
       docs/api/invert4geom.optimization.rst|
       CHANGELOG.md|
+      .github/ISSUE_TEMPLATE/bug_report.md|
+      .github/ISSUE_TEMPLATE/feature_request.md|
+      .github/config.yml|
   )$
 
 repos:
@@ -90,6 +93,7 @@ repos:
     hooks:
       - id: shellcheck
 
+  # check for commonly miss-capitalized words
   - repo: local
     hooks:
       - id: disallow-caps

docs/conf.py

@@ -40,17 +40,17 @@
     #
     # Runtime deps
     #
-    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("http://pandas.pydata.org/pandas-docs/stable/", None),
-    "xarray": ("http://xarray.pydata.org/en/stable/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
     "verde": ("https://www.fatiando.org/verde/latest/", None),
     "rioxarray": ("https://corteva.github.io/rioxarray/stable/", None),
     # pykdtree
     "xrft": ("https://xrft.readthedocs.io/en/stable/", None),
     "harmonica": ("https://www.fatiando.org/harmonica/latest/", None),
     "antarctic_plots": ("https://antarctic-plots.readthedocs.io/en/latest/", None),
     "numba": ("https://numba.pydata.org/numba-doc/latest/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     # nptyping
     # numba_progress
     # "tqdm": ("https://tqdm.github.io/", None),
@@ -61,7 +61,7 @@
     "pyvista": ("https://docs.pyvista.org/", None),
     # trame
     # ipywidgets
-    "matplotlib": ("https://matplotlib.org/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
     "seaborn": ("https://seaborn.pydata.org/", None),
     #
     # Opti deps

docs/contributing.md

@@ -0,0 +1,3 @@
+```{include} ../.github/CONTRIBUTING.md
+
+```

docs/index.md

@@ -52,14 +52,14 @@ gallery/index.md
 api/invert4geom
 citing.md
 changelog.md
-references.md
+references.rst
 ```
 
 ```{toctree}
 :maxdepth: 1
 :hidden:
 :caption: ℹ️ Other resources
-How to contribute <https://github.com/mdtanker/invert4geom/blob/main/.github/CONTRIBUTING.md>
+contributing.md
 Source code on GitHub <https://github.com/mdtanker/invert4geom>
 ```
 
@@ -120,7 +120,7 @@ make changes to the ones we already have while we try to improve the
 software based on users' experience, test new ideas, take better design
 decisions, etc.
 Some of these changes could be **backwards incompatible**. Keep that in
-mind before you update Harmonica to a newer version.
+mind before you update Invert4Geom to a newer version.
 ```
 
 ```{admonition} How to contribute

docs/overview.md

@@ -91,11 +91,11 @@ in the **Regional** module for finding the optimal regional separation methods.
 
 ## Plotting
 
-Various function for plotting maps and graphs used throughout the other modules
+Various function for plotting maps and graphs used throughout the other modules.
 
 ## Utils
 
-Utilities used throughout the other modules
+Utilities used throughout the other modules.
 
 ## Synthetic
 

env/RTD_env.yml

@@ -1,4 +1,4 @@
-# Requirements for running the github action: test only need run-time dependencies
+# Requirements for building the documentation
 name: invert4geom
 channels:
   - conda-forge
@@ -24,10 +24,10 @@ dependencies:
   - pygmt
   - dask
   # opti
-  - optuna>=3.1.0
-  - botorch>=0.4.0
-  - psutil
-  - joblib
+  # - optuna>=3.1.0
+  # - botorch>=0.4.0
+  # - psutil
+  # - joblib
   # docs
   - sphinx>=4.0
   - myst-parser

noxfile.py

@@ -80,7 +80,7 @@ def docs(session: nox.Session) -> None:
 
     extra_installs = ["sphinx-autobuild"] if args.serve else []
 
-    session.install("-e.[opti,docs,viz]", *extra_installs)
+    session.install("-e.[docs]", *extra_installs)
     session.chdir("docs")
 
     if args.builder == "linkcheck":

pyproject.toml

@@ -27,6 +27,7 @@ classifiers = [
 ]
 readme = "README.md"
 version = "0.3.0"
+license = {file = "LICENSE"}
 
 dependencies = [
   "numpy",

src/invert4geom/inversion.py

@@ -97,17 +97,17 @@ def jacobian_annular(
     jac: NDArray,
 ) -> NDArray:
     """
-        Function to calculate the Jacobian matrix using the annular cylinder
-        approximation. The resulting Jacobian is a matrix (numpy array) with a row per
-        gravity observation and a column per prism. This approximates the prisms as an
-        annulus, and calculates it's vertical gravity derivative. Takes arrays from
-        `jacobian`, feeds them into `grav_column_der`, and returns the jacobian.
+    Function to calculate the Jacobian matrix using the annular cylinder
+    approximation. The resulting Jacobian is a matrix (numpy array) with a row per
+    gravity observation and a column per prism. This approximates the prisms as an
+    annulus, and calculates it's vertical gravity derivative. Takes arrays from
+    `jacobian`, feeds them into `grav_column_der`, and returns the jacobian.
 
     Parameters
     ----------
     grav_easting, grav_northing, grav_upward : NDArray
-        coordinates of gravity observation points.
-    prism_easting, prism_northing, prism_top, : NDArray
+        coordinates of gravity observation points
+    prism_easting, prism_northing, prism_top : NDArray
         coordinates of prism's center in northing, easting, and upward directions,
         respectively
     prism_density : NDArray

src/invert4geom/optimization.py

@@ -69,7 +69,7 @@ def available_cpu_count() -> typing.Any:
     # cpuset may restrict the number of *available* processors
     try:
         # m = re.search(r"(?m)^Cpus_allowed:\s*(.*)$", open("/proc/self/status").read())
-        with pathlib.Path("/proc/self/status").open() as f:  # pylint: disable=unspecified-encoding
+        with pathlib.Path("/proc/self/status").open(encoding="utf8") as f:
             m = re.search(r"(?m)^Cpus_allowed:\s*(.*)$", f.read())
         if m:
             res = bin(int(m.group(1).replace(",", ""), 16)).count("1")
@@ -138,7 +138,7 @@ def available_cpu_count() -> typing.Any:
     # Linux
     try:
         # res = open("/proc/cpuinfo").read().count("processor\t:")
-        with pathlib.Path("/proc/cpuinfo").open() as f:  # pylint: disable=unspecified-encoding
+        with pathlib.Path("/proc/cpuinfo").open(encoding="utf8") as f:
             res = f.read().count("processor\t:")
 
         if res > 0:
@@ -163,7 +163,7 @@ def available_cpu_count() -> typing.Any:
     try:
         try:
             # dmesg = open("/var/run/dmesg.boot").read()
-            with pathlib.Path("/var/run/dmesg.boot").open() as f:  # pylint: disable=unspecified-encoding
+            with pathlib.Path("/var/run/dmesg.boot").open(encoding="utf8") as f:
                 dmesg = f.read()
             # dmesg = pathlib.Path("/var/run/dmesg.boot").open().read()
         except OSError: