Merge branch 'main' into docs

Author: mdtanker

.github/workflows/ci.yml

@@ -63,7 +63,7 @@ jobs:
 
       # Install Micromamba with conda-forge dependencies
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: env/testing_env.yml
           create-args: >-
@@ -83,6 +83,6 @@ jobs:
           pytest -ra --cov --cov-report=xml --cov-report=term --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -39,7 +39,7 @@ repos:
         exclude: \.md
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.0"
+    rev: "v0.6.9"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -48,7 +48,7 @@ repos:
         exclude: \.md
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
+    rev: "v5.0.0"
     hooks:
       - id: check-added-large-files
         exclude: ^(docs/examples/bishop_basement_model.ipynb|docs/tutorial/05_density_optimization.ipynb|docs/tutorial/06_reference_level_optimization.ipynb|docs/examples/uieda_et_al_2017_CRUST1.ipynb|docs/quickstart.ipynb|docs/tutorial/02_simple_inversion.ipynb|docs/tutorial/08_combining_it_all.ipynb)
@@ -80,7 +80,7 @@ repos:
         exclude: \.md
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.10.1"
+    rev: "v1.11.2"
     hooks:
       - id: mypy
         files: src|tests
@@ -116,13 +116,13 @@ repos:
         exclude: .pre-commit-config.yaml
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: "v0.18"
+    rev: "v0.20.2"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.29.0"
+    rev: "0.29.3"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

CHANGELOG.md

@@ -4,11 +4,44 @@ Automatically updated by
 with commit parsing of [angular commits](https://github.com/angular/angular.js/blob/master/DEVELOPERS.md#commits).
 
 ## Unreleased
+### 🧰 Chores / Maintenance
+* bump binder env to v.0.10 ([`0604561`](https://github.com/mdtanker/invert4geom/commit/060456170989616a09aa5824815194ee60061804))
+* update release checklist and make commands ([`8943bd0`](https://github.com/mdtanker/invert4geom/commit/8943bd04fbd076b48d379ab325e1e7969c740bf5))
+### 📖 Documentation
+* update some docs notebooks ([`6fe1488`](https://github.com/mdtanker/invert4geom/commit/6fe1488d7cda52615d7890cf11c4811b637d17fd))
+
+
+## v0.10.0 (2024-10-09)
+### 📦️ Build
+* make xesmf optional dependency ([`8f3494c`](https://github.com/mdtanker/invert4geom/commit/8f3494c66d3cb3d0999c55b56fe148fcfcc81c62))
+### 🧰 Chores / Maintenance
+* set ruff rule ([`7cdb2b0`](https://github.com/mdtanker/invert4geom/commit/7cdb2b0b6dffd3567f1277e94f1a88fd0b24562f))
+### 📖 Documentation
+* update and rerun doc notebooks ([`7285281`](https://github.com/mdtanker/invert4geom/commit/728528117ce62b3536fc20cbcaf76c23b5080406))
+### 🚀 Features
+* allow passing column name for weights in create_topography ([`1815139`](https://github.com/mdtanker/invert4geom/commit/18151399629e2b0fda306171577510250d38fee1))
+* add fname option to optimize functions ([`1bb69b6`](https://github.com/mdtanker/invert4geom/commit/1bb69b6044ed1c6149d7f3b083debf19d97d7040))
+### 🐛 Bug Fixes
+* minor changes ([`338306d`](https://github.com/mdtanker/invert4geom/commit/338306dd5d0f9b8349f5a93cc4585a0c65097eaa))
+* re-write long-wavelength contamination function, adding dependency xesmf ([`6e96870`](https://github.com/mdtanker/invert4geom/commit/6e968709a11cc28039d08695a83206f64a7c51fb))
+* add debug for eq source fitting ([`43e2855`](https://github.com/mdtanker/invert4geom/commit/43e28559184a38da218acf849bcbe02dae83a622))
+* if too few points, reduce K folds until it works for fitting Splines ([`5d40917`](https://github.com/mdtanker/invert4geom/commit/5d40917f3f0bc3e470f4c13a7ebdc1994275a490))
+* re-create starting topography for each fold of training constraint points in density/zref optimization ([`5da58fb`](https://github.com/mdtanker/invert4geom/commit/5da58fbcf8a091506636f19f7755853e506bfbf4))
+* bug for checking gravity inside topo region with density/zref cv ([`e96099a`](https://github.com/mdtanker/invert4geom/commit/e96099a3b18e44a34885e852cabef9054209ee47))
+### ✏️ Formatting
+* pre-commit fixes ([`7802143`](https://github.com/mdtanker/invert4geom/commit/7802143f8bea1ee0101540b5ee88f21011b937ff))
+* pre-commit fixes ([`28687c5`](https://github.com/mdtanker/invert4geom/commit/28687c597d4c956ac4adabf691084061c13313e8))
+
+## v0.9.1 (2024-10-03)
 ### 📦️ Build
 * add pooch and scikit-learn as dependencies ([`8bebf45`](https://github.com/mdtanker/invert4geom/commit/8bebf4545ad816fddc25d59d91dcc578019c86ca))
 ### 🧰 Chores / Maintenance
 * update binder env to `v0.9` ([`0307bd9`](https://github.com/mdtanker/invert4geom/commit/0307bd9f38c5f20d83eeab8e73c9e5dd0b1f5f4e))
-
+### 📖 Documentation
+* update and rerun docs ([`1d39529`](https://github.com/mdtanker/invert4geom/commit/1d39529ee0b9bbf11eea7e32a87e2a710b1fa887))
+### 🐛 Bug Fixes
+* fixes error of using 1x not 4.5x default depth for eq sources ([`5746851`](https://github.com/mdtanker/invert4geom/commit/57468519286d34691f06855e9d278f8ee2a598d0))
+* enable `default` eq source depth for regional constraints ([`d9301a3`](https://github.com/mdtanker/invert4geom/commit/d9301a3394e4a54b171a245d8bd0af7821c11c98))
 
 ## v0.9.0 (2024-08-10)
 ### 📦️ Build

Makefile

@@ -13,14 +13,14 @@ create:
 install:
 	pip install -e .[all]
 
-install_test:
-	pip install $(PROJECT)[all]
-
 remove:
 	mamba remove --name $(PROJECT) --all
 
+pip_install:
+	pip install $(PROJECT)[all]
+
 conda_install:
-	mamba create --name $(PROJECT) --yes --force --channel conda-forge $(PROJECT) pytest pytest-cov
+	mamba create --name $(PROJECT) --yes --force --channel conda-forge $(PROJECT) pytest pytest-cov ipykernel
 
 ####
 ####

binder/environment.yml

@@ -3,7 +3,6 @@ channels:
   - conda-forge
 dependencies:
   - python==3.11
-  - geopandas==0.14
   - pip
   - pip:
-    - invert4geom==0.9
+    - invert4geom==0.10

docs/contributing.md

@@ -399,13 +399,21 @@ Now, when submitting a PR, `RTD` will automatically build the docs and update th
 
 ## Release Checklist
 * re-run any relevant notebooks
-* add any new dependencies to the binder env
 * check docs are building correctly using the GitHub actions link within the PR
 * merge the PR
 * wait for `PyPI` to publish the new version [here](https://pypi.python.org/pypi/invert4geom)
 * wait for a PR to be opened in the [feedstock](https://github.com/conda-forge/invert4geom-feedstock)
 * update any changed dependencies in the feedstock PR and merge
 * wait for `conda` to publish the new version [here](https://anaconda.org/conda-forge/invert4geom)
 * update invert4geom version in `binder/environment.yml`.
-* test `PyPI` version with `make install_test` and `make test`
-* test `conda` version with `make conda_install` and `make test`
+* test `PyPI` version with:
+    - `make remove`
+    - `make create`
+    - `mamba activate invert4geom`
+    - `make pip_install`
+    - `make test`
+* test `conda` version with:
+    - `make remove`
+    - `make conda_install`
+    - `mamba activate invert4geom`
+    - `make test`