Merge Pre release branch onto main (#84)

* new fault_system_solution_helper module
* a simple rupture grouping algo;
* drop_zero_rate differentiates between FSS and IS;
* refactor subsection filter & tests
* migrate to filter_rupture_ids.for_subsections();
* migrate to filter_rupture_ids.for_parent_fault_ids();
* fixed method names; added doc page for subsection_id_filter;
* refactor filter tests; WIP on DeprecationWarnings; new filter_parent_fault_ids; detox
* fixing many deprecation warnings; updated geopandas, pandas, numpy, pyvista libs; changes to read_csv_dtype configuration; detox
* refactor filters int package; more test cover; implement new filters; migrate old functions and deprecate warn the originals;
* unifying filter methods; improve docstrings & tests;
* implement rate and mag filtering on rupture_id_filter;
* migrate find rupture polygons into filter class; move drop_zero_rates into class init;
* implement ChainableSetBase; migrate FilterRuptureIds to be chainable;
* add set operation support for chaining (join_prior) and test coverage;
* join arguments tidied up; strings and ENUMS are supported;
* fix set operand method names;
* fix set operations return type
* implement set operands for supported set methods; improve docs
* merge 3d geometry changes from @voj; add some testing;
* new participation rate functions; detox
* test 3d surfaces
* migrate participation functions into classes proper; add FSS section_participation;
* make subsection_id_filter chainable;
* added participation methods to fault_system_solution
* simplify FSS participation using rate_weighted_mean; refactor dataframe dtypes; participation performance testing;
* standardise participation functions API and return column;
* fix rate_column; add .all() methods to filter classes;
* add TinyInversionSolution fixture; tune pytest fixture scoping for massive test speed up (~3 times faster);
* doc and docstrings improvements; Better typing in filter package;
* more on rupture_grouping
* add module docstring to inversion_solution_file;
* adding dataframe schema validations with panderas;
* WIP, adding InversionSolutionFile::RuptureRateSchema;
* Feature/52 refactor inversion solution (#53)
* Chore/54 test coverage (#55)
* Chore/59 doc fixes (#61)
* make parent fault filter chainable (#66)
* fix for #57 (return int type for polygons);
* update pytz dep (#69)
* Feature/49 named fault participation (#67)
* Feature: named_fault_participation_rate #49
* Epic Feature: enhanced participation rate options #42
* refactor to remove *Protocol superclasses (#73)
* refactor to remove *Protocol superclasses; migrate and improve docstrings; detox
* Feature/71 scale rupture rates (#74)
* fold in changes suggested by @chrisdicaprio on PR #73;
* fix drop_zero_rates on FilterRuptureIds.for_magnitude(); 
* fix for_parent_fault_ids
* fix test_ruptures_for_subsections
* fix for_rupture_rate
* fix for_polygon ; fix impacted tests;
* Bump version: 0.13.0 → 1.0.0-alpha
* add joint_type arg to relevant FilterRuptureId class methods (#80)
* add joint_type arg to `for_parent_fault_names` *  `for_parent_fault_ids`; add tolist() convenience method;
* refactor for readability/efficiency; add full test coverage for new arg;
* add `join_type` arg to `for_subsection_ids` (working but a little slow); detox;
* rename arg for consistency
* refactoring; new docstrings; named_faults support; detox;
* remove commented line
* changelog entry;
* Bump version: 1.0.0-alpha → 1.0.0-beta
* align version ids
* Chore/82 make docs and api align (#83)
* Bump version: 1.0.0-beta-0 → 1.0.0

---------

Co-authored-by: Chris DiCaprio <[email protected]>

Author: chrisbc

.bumpversion.cfg

@@ -1,7 +1,23 @@
 [bumpversion]
-current_version = 0.12.3
+current_version = 1.0.0
 commit = True
 tag = True
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(-(?P<release>.*)-(?P<build>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}-{build}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+first_value = regular
+optional_value = regular
+values = 
+	alpha
+	beta
+	rc
+	test
+	regular
+
+[bumpversion:part:build]
 
 [bumpversion:file:pyproject.toml]
 search = version = "{current_version}"

.github/workflows/run-tests.yml

@@ -22,14 +22,16 @@ jobs:
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-versions }}
 
       - name: Install and configure Poetry
         uses: GNS-Science/install-poetry@main
+        # uses: snok/install-poetry@v1
         with:
+          version: 1.8.4
           virtualenvs-create: true
           virtualenvs-in-project: true
           installer-parallel: true
@@ -39,7 +41,7 @@ jobs:
       #----------------------------------------------
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}-run-tests
@@ -49,8 +51,12 @@ jobs:
       #----------------------------------------------
       - name: Install dependencies
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: |
+        run:
           poetry install --no-interaction --no-root --with dev --all-extras
+
+      - name: Install tox-gh-actions
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run:
           poetry add tox-gh-actions
 
       - name: test with tox (uses tox-gh-actions to select correct environment)
@@ -61,7 +67,7 @@ jobs:
         run: ls -l .
 
       - name: Submit coverage report
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           files: ./coverage.xml # optional
           flags: unittests # optional

CHANGELOG.md

@@ -1,5 +1,59 @@
 # Changelog
 
+## [1.0.0] 2025-02-27
+ - version update for v1.0.0 release
+
+## [1.0.0-beta-0] 2025-02-27
+## Changed
+ - 'refactored the usage docs
+
+## Added
+ - `join_type` argument as needed in `FilterRutpureId` methods.
+
+# Removed
+ - methods are no longer exported from the top-level package.
+
+## [1.0.0-alpha] 2025-02-20
+
+## Changed
+ - drop_zero_rate differentiates between FSS and IS;
+ - faster testing (~3 times faster)
+ - documentation improvements
+ - fix many deprecation warnings
+ - updated dependencies: geopandas, pandas, numpy, pyvista libs
+ - read_csv dtype configuration improvements
+ - many old functions are deprecated/migrated to new filter package
+ - refactor dataframe dtypes
+ - standardise participation functions API and return columns
+ - refactor `solvis.inversion_solution` package to `solvis.solution` and collect modules into packages
+ - new packages `solvis.solution.inversion_solution` and  `solvis.solution.fault_system_solution`
+ - improved test coverage
+ - refactored to/from archive code to reinstate some skipped tests
+ - doc/typing improvements
+ - fixes to the dynamic docstrings helper class & setup
+ - API simplifications
+ - updated flake8 and applied many docstring fixes.
+ - refactored participation methods into module/class.
+ - use valid NSHM fault names in docstring examples.
+ - `FilterParentFaultIds` class is now chainable, like the other filters.
+ - fix for #77 (drop_zero_rates is ignored)
+
+## Added
+ - new filter package providing classes for filtering solutions
+ - support for 3d geometry (thanks @voj)
+ - simplify FSS participation using rate_weighted_mean
+ - participation performance testing;
+ - added participation methods to fault_system_solution
+ - a simple rupture grouping algorithm (can this be a different type of filter??);
+ - `pandera` library for dataframe model validations and better docs
+ - ChainableSet now supports set.symmetric_difference
+ - named_fault support in filtering and solution participation.
+ - new scale_rupture_rates() method on InversionSolution
+
+## Removed
+ - deprecated `solvis.solvis` functions removed.
+ - deprecated `solvis.inversion_solution.*` functions/methods removed.
+
 ## [0.12.3] 2024-07-04
 bump version to verify new pypi workflow
 

docs/api/filter/chainable_set_base.md

@@ -0,0 +1 @@
+::: solvis.filter.chainable_set_base

docs/api/filter/index.md

@@ -0,0 +1,3 @@
+::: solvis.filter
+<!--     options:
+        show_root_heading: false -->

docs/api/filter/parent_fault_id_filter.md

@@ -0,0 +1 @@
+::: solvis.filter.parent_fault_id_filter

docs/api/filter/rupture_id_filter.md

@@ -0,0 +1 @@
+::: solvis.filter.rupture_id_filter

docs/api/filter/subsection_id_filter.md

@@ -0,0 +1 @@
+::: solvis.filter.subsection_id_filter