merge develop

Author: dilpath

.github/workflows/ci_tests.yml

@@ -17,10 +17,10 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -31,7 +31,7 @@ jobs:
       shell: bash
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ steps.pip_cache_dir.outputs.dir }}
         key: ${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/.ci_pip_reqs.txt') }}-${{ hashFiles('**/setup.py') }}
@@ -51,7 +51,7 @@ jobs:
       run: tox -e unit
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

.github/workflows/deploy.yml

@@ -15,9 +15,9 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Set up python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.11
 

.readthedocs.yaml

@@ -5,7 +5,7 @@ version: 2
 
 sphinx:
    configuration: doc/conf.py
-   fail_on_warning: true
+   fail_on_warning: false
 
 build:
   os: "ubuntu-22.04"

CHANGELOG.md

@@ -1,5 +1,71 @@
 # PEtab changelog
 
+## 0.4 series
+
+### 0.4.0
+
+**Prepare for PEtab v2**
+
+To enable ongoing support for PEtab v1, while "forking" the v1 code for PEtab v2, the old code base is now available at `petab.v1`, and the new code base will be at `petab.v2`. For now, old `import petab.*` statements still work, but are marked as deprecated, and `import petab.v1.*` should be used instead. `petablint` will be designed for use with only full PEtab problems in future too, rather than individual tables -- partial problems will be supported to validate individual tables.
+
+* Add PEtab math parser and sympy converter by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/260
+* Deprecate petablint with individual tables by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/274
+* Introduce petab.v1 package by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/282
+* Separate v1 and v2 tests by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/284
+* Add petab.v2.Problem by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/285
+* PEtab v1 to v2 converter by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/281
+* Fix imports related to v1 subpackage by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/293
+
+**Validation**
+
+Validation will become increasingly atomic and OOP, to support extension-specific validation in PEtab v2.
+
+* Validator: check for positive bounds for log-scaled parameter by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/278
+* Validator: check prior parameters by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/279
+* Fix validation for remote files by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/287
+* New validation API by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/288
+
+**Documentation**
+
+* Fixed formatting / missing type annotations by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/292
+* Added versioning and deprecation policy by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/277
+
+**Other changes**
+
+* Simplify yaml schema by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/264
+* Handle numpy types in sympify_petab by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/294
+* New `get_path_prefix` method to get the base path for relative paths in PEtab problem YAML by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/280
+
+**New Contributors**
+
+* @dependabot made their first contribution in https://github.com/PEtab-dev/libpetab-python/pull/267
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.3.0...v0.4.0
+
+## 0.3 series
+
+### 0.3.0
+
+**This release requires `python>=3.10`**
+
+**Features**
+* Visualization: Make line plot lines configurable via
+  `petab.visualize.plotter.measurement_line_kwargs and
+  `petab.visualize.plotter.simulation_line_kwargs`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/254
+* Validator: check that `datasetId`s referenced in visualization tables exists
+  in measurement tables
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/255
+
+**Fixes**
+* Drop an index if it's reset
+  by @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/262
+
+## New Contributors
+* @PaulJonasJost made their first contribution in https://github.com/PEtab-dev/libpetab-python/pull/250
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.2.9...v0.3.0
+
 ## 0.2 series
 
 ### 0.2.9

MANIFEST.in

@@ -1,2 +1,3 @@
 recursive-include petab/schemas *.yaml
-recursive-include petab/visualize/templates *
+recursive-include petab/v1/visualize/templates *
+recursive-exclude tests *

README.md

@@ -39,11 +39,11 @@ be:
     entrypoints to be available as a shell command from anywhere, called
     `petablint`
 
-  - [`petab.create_parameter_df`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.parameters.html#petab.parameters.create_parameter_df)
+  - [petab.create_parameter_df](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.parameters.html#petab.parameters.create_parameter_df)
     to create the parameter table, once you have set up the model,
     condition table, observable table and measurement table
 
-  - [`petab.create_combine_archive`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.core.html#petab.core.create_combine_archive)
+  - [petab.create_combine_archive](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.core.html#petab.core.create_combine_archive)
     to create a [COMBINE Archive](https://combinearchive.org/index/) from PEtab
     files
 

doc/development.rst

@@ -0,0 +1,26 @@
+Development
+===========
+
+Versioning
+----------
+
+We use `Semantic Versioning <http://semver.org/>`_ with the modifications
+described under :ref:`deprecation_policy`.
+
+.. _deprecation_policy:
+
+Deprecation policy
+------------------
+
+petab aims to provide a stable API for users. However, not all features can be
+maintained indefinitely. We will deprecate features in minor releases and
+where possible, issue a warning when they are used. We will keep deprecated
+features for at least six months after the release that includes the
+respective deprecation warning and then remove them earliest in the next minor
+or major release. If a deprecated feature is the source of a major bug, we may
+remove it earlier.
+
+Python compatibility
+--------------------
+
+We follow `numpy's Python support policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_.

doc/index.rst

@@ -14,6 +14,7 @@
    Changelog <CHANGELOG.md>
    how_to_cite
    license
+   development
 
 .. toctree::
    :maxdepth: 2

doc/modules.rst

@@ -1,28 +1,32 @@
 API Reference
 =============
 
-.. automodule:: petab
-
 .. rubric:: Modules
 
 .. autosummary::
    :toctree: build/_autosummary
    :recursive:
 
-   petab.C
-   petab.calculate
-   petab.composite_problem
-   petab.conditions
-   petab.core
-   petab.lint
-   petab.measurements
-   petab.observables
-   petab.parameter_mapping
-   petab.parameters
-   petab.problem
-   petab.sampling
-   petab.sbml
-   petab.simulate
-   petab.simplify
-   petab.visualize
-   petab.yaml
+   petab
+   petab.v1
+   petab.v1.C
+   petab.v1.calculate
+   petab.v1.composite_problem
+   petab.v1.conditions
+   petab.v1.core
+   petab.v1.lint
+   petab.v1.measurements
+   petab.v1.models
+   petab.v1.observables
+   petab.v1.parameter_mapping
+   petab.v1.parameters
+   petab.v1.problem
+   petab.v1.sampling
+   petab.v1.sbml
+   petab.v1.simulate
+   petab.v1.simplify
+   petab.v1.visualize
+   petab.v1.yaml
+   petab.v2
+   petab.v2.lint
+   petab.v2.problem