🚧🚀🚇♻️ Shape up for release

.github/workflows/integration-tests.yml

@@ -0,0 +1,48 @@
+name: "Run Examples"
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  run-examples:
+    name: "Run Example: "
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        example_name:
+          [
+            quick-start,
+            fluorescence,
+            transient-absorption,
+            transient-absorption-two-datasets,
+            spectral-constraints,
+            spectral-guidance,
+            two-datasets,
+            sim-3d-disp,
+            sim-3d-nodisp,
+            sim-3d-weight,
+            sim-6d-disp,
+          ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install pyglotaran-extras
+        run: |
+          pip install wheel
+          pip install .
+      - name: ${{ matrix.example_name }}
+        id: example-run
+        uses: glotaran/pyglotaran-examples@main
+        with:
+          example_name: ${{ matrix.example_name }}
+          install_extras: false
+      - name: Upload Example Plots Artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: example-plots
+          path: ${{ steps.example-run.outputs.plots-path }}

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
       - id: absolufy-imports
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.26.0
+    rev: v2.29.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
@@ -36,13 +36,13 @@ repos:
         minimum_pre_commit_version: 2.9.0
 
   - repo: https://github.com/asottile/yesqa
-    rev: v1.2.3
+    rev: v1.3.0
     hooks:
       - id: yesqa
         additional_dependencies: [flake8-docstrings]
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.17.0
+    rev: v1.18.0
     hooks:
       - id: setup-cfg-fmt
 
@@ -76,7 +76,7 @@ repos:
   # Linters
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910
+    rev: v0.910-1
     hooks:
       - id: mypy
         exclude: ^docs
@@ -90,7 +90,7 @@ repos:
   #       pass_filenames: false
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
+    rev: 4.0.1
     hooks:
       - id: flake8
         args:
@@ -111,5 +111,6 @@ repos:
     rev: v2.1.0
     hooks:
       - id: codespell
-        files: ".py|.rst"
-        args: [-L pyglotaran]
+        types: [file]
+        types_or: [python, pyi, markdown, rst, jupyter]
+        args: ["--ignore-words-list=doas"]

pyglotaran_extras/__init__.py

@@ -1 +1,19 @@
-__version__ = "0.3.3"
+from pyglotaran_extras.io.load_data import load_data
+from pyglotaran_extras.io.setup_case_study import setup_case_study
+from pyglotaran_extras.plotting.plot_data import plot_data_overview
+from pyglotaran_extras.plotting.plot_overview import plot_overview
+from pyglotaran_extras.plotting.plot_overview import plot_simple_overview
+from pyglotaran_extras.plotting.plot_traces import plot_fitted_traces
+from pyglotaran_extras.plotting.plot_traces import select_plot_wavelengths
+
+__all__ = [
+    "load_data",
+    "setup_case_study",
+    "plot_data_overview",
+    "plot_overview",
+    "plot_simple_overview",
+    "plot_fitted_traces",
+    "select_plot_wavelengths",
+]
+
+__version__ = "0.5.0rc1"

pyglotaran_extras/deprecation/__init__.py

@@ -0,0 +1,4 @@
+"""Module containing deprecation functionality."""
+from pyglotaran_extras.deprecation.deprecation_utils import warn_deprecated
+
+__all__ = ["warn_deprecated"]

pyglotaran_extras/deprecation/deprecation_utils.py

@@ -0,0 +1,152 @@
+from __future__ import annotations
+
+from importlib.metadata import distribution
+from warnings import warn
+
+FIG_ONLY_WARNING = (
+    "In the future plot functions which create figures, will return a tuple "
+    "of Figure AND the Axes. Please set ``figure_only=False`` and adjust your code.\n"
+    "This usage will be an error in version: 0.7.0."
+)
+
+
+class OverDueDeprecation(Exception):
+    """Error thrown when a deprecation should have been removed.
+
+    See Also
+    --------
+    deprecate
+    warn_deprecated
+    deprecate_module_attribute
+    deprecate_submodule
+    deprecate_dict_entry
+    """
+
+
+class PyglotaranExtrasApiDeprecationWarning(UserWarning):
+    """Warning to give users about API changes.
+
+    See Also
+    --------
+    warn_deprecated
+    """
+
+
+def pyglotaran_extras_version() -> str:
+    """Version of the distribution.
+
+    This is basically the same as ``pyglotaran_extras.__version__`` but independent
+    from pyglotaran_extras.
+    This way all of the deprecation functionality can be used even in
+    ``pyglotaran_extras.__init__.py`` without moving the import below the definition of
+    ``__version__`` or causeing a circular import issue.
+
+    Returns
+    -------
+    str
+        The version string.
+    """
+    return distribution("pyglotaran-extras").version
+
+
+def parse_version(version_str: str) -> tuple[int, int, int]:
+    """Parse version string to tuple of three ints for comparison.
+
+    Parameters
+    ----------
+    version_str : str
+        Fully qualified version string of the form 'major.minor.patch'.
+
+    Returns
+    -------
+    tuple[int, int, int]
+        Version as tuple.
+
+    Raises
+    ------
+    ValueError
+        If ``version_str`` has less that three elements separated by ``.``.
+    ValueError
+        If ``version_str`` 's first three elements can not be casted to int.
+    """
+    error_message = (
+        "version_str needs to be a fully qualified version consisting of "
+        f"int parts (e.g. '0.0.1'), got {version_str!r}"
+    )
+    split_version = version_str.partition("-")[0].split(".")
+    if len(split_version) < 3:
+        raise ValueError(error_message)
+    try:
+        return tuple(
+            map(int, (*split_version[:2], split_version[2].partition("rc")[0]))
+        )  # type:ignore[return-value]
+    except ValueError:
+        raise ValueError(error_message)
+
+
+def check_overdue(deprecated_qual_name_usage: str, to_be_removed_in_version: str) -> None:
+    """Check if a deprecation is overdue for removal.
+
+    Parameters
+    ----------
+    deprecated_qual_name_usage : str
+        Old usage with fully qualified name e.g.:
+        ``'glotaran.read_model_from_yaml(model_yml_str)'``
+    to_be_removed_in_version : str
+        Version the support for this usage will be removed.
+
+    Raises
+    ------
+    OverDueDeprecation
+        If the current version is greater or equal to ``to_be_removed_in_version``.
+    """
+    if (
+        parse_version(pyglotaran_extras_version()) >= parse_version(to_be_removed_in_version)
+        and "dev" not in pyglotaran_extras_version()
+    ):
+        raise OverDueDeprecation(
+            f"Support for {deprecated_qual_name_usage.partition('(')[0]!r} was "
+            f"supposed to be dropped in version: {to_be_removed_in_version!r}.\n"
+            f"Current version is: {pyglotaran_extras_version()!r}"
+        )
+
+
+def warn_deprecated(
+    *,
+    deprecated_qual_name_usage: str,
+    new_qual_name_usage: str,
+    to_be_removed_in_version: str,
+    stacklevel: int = 2,
+) -> None:
+    """Raise deprecation warning with change information.
+
+    The change information are old / new usage information and end of support version.
+
+    Parameters
+    ----------
+    deprecated_qual_name_usage : str
+        Old usage with fully qualified name e.g.:
+        ``'glotaran.read_model_from_yaml(model_yml_str)'``
+    new_qual_name_usage : str
+        New usage as fully qualified name e.g.:
+        ``'glotaran.io.load_model(model_yml_str, format_name="yml_str")'``
+    to_be_removed_in_version : str
+        Version the support for this usage will be removed.
+
+    stacklevel: int
+        Stack at which the warning should be shown as raise. Default: 2
+
+    Raises
+    ------
+    OverDueDeprecation
+        If the current version is greater or equal to ``to_be_removed_in_version``.
+    """
+    check_overdue(deprecated_qual_name_usage, to_be_removed_in_version)
+    warn(
+        PyglotaranExtrasApiDeprecationWarning(
+            f"Usage of {deprecated_qual_name_usage!r} was deprecated, "
+            f"use {new_qual_name_usage!r} instead.\n"
+            f"This usage will be an error in version: {to_be_removed_in_version!r}."
+        ),
+        stacklevel=stacklevel,
+    )

pyglotaran_extras/io/__init__.py

@@ -1,2 +1,5 @@
 """ pyglotaran-extras io package """
-from pyglotaran_extras.io.boilerplate import setup_case_study
+from pyglotaran_extras.io.load_data import load_data
+from pyglotaran_extras.io.setup_case_study import setup_case_study
+
+__all__ = ["setup_case_study", "load_data"]

pyglotaran_extras/io/boilerplate.py

@@ -1,81 +1,12 @@
-from __future__ import annotations
-
-import inspect
-from os import PathLike
-from pathlib import Path
-
-
-def setup_case_study(
-    output_folder_name: str = "pyglotaran_results",
-    results_folder_root: None | str | PathLike[str] = None,
-) -> tuple[Path, Path]:
-    """Convenience function to to quickly get folders for a case study.
-
-    This is an execution environment independent (works in python script files
-    and notebooks, independent of where the python runtime was called from)
-    way to get the folder the analysis code resides in and also creates the
-    ``results_folder`` in case it didn't exist before.
-
-    Parameters
-    ----------
-    output_folder_name : str
-        Name of the base folder for the results., by default "pyglotaran_results"
-    results_folder_root : None
-        Parent folder the ``output_folder_name`` should be put in
-        , by default None which results in the users Home folder being used
-
-    Returns
-    -------
-    tuple[Path, Path]
-        results_folder, script_folder:
-
-        results_folder:
-            Folder to be used to save results in of the pattern
-            (``results_folder_root`` / ``output_folder_name`` / ``analysis_folder.parent``).
-        analysis_folder:
-            Folder the script or Notebook resides in.
-    """
-    analysis_folder = get_script_dir(nesting=1)
-    print(f"Setting up case study for folder: {analysis_folder}")
-    if results_folder_root is None:
-        results_folder_root = Path.home() / output_folder_name
-    else:
-        results_folder_root = Path(str(results_folder_root))
-    script_folder_rel = analysis_folder.relative_to(analysis_folder.parent)
-    results_folder = (results_folder_root / script_folder_rel).resolve()
-    results_folder.mkdir(parents=True, exist_ok=True)
-    print(f"Results will be saved in: {results_folder}")
-    return results_folder, analysis_folder.resolve()
-
-
-def get_script_dir(*, nesting: int = 0) -> Path:
-    """Gets parent folder a script is executed in.
-
-    This is a helper function for cross compatibility with jupyter notebooks.
-    In notebooks the global ``__file__`` variable isn't set, thus we need different
-    means to get the folder a script is defined in, which doesn't change with the
-    current working director the ``python interpreter`` was called from.
-
-    Parameters
-    ----------
-    nesting : int
-        Number to go up in the call stack to get to the initially calling function.
-        This is only needed for library code and not for user code.
-        , by default 0 (direct call)
-
-    Returns
-    -------
-    Path
-        Path to the folder the script was resides in.
-
-    See Also
-    --------
-    setup_case_study
-    """
-    calling_frame = inspect.stack()[nesting + 1].frame
-    file_var = calling_frame.f_globals.get("__file__", ".")
-    file_path = Path(file_var).resolve()
-    if file_var == ".":  # pragma: no cover
-        return file_path
-    else:
-        return file_path.parent
+"""Deprecated module."""
+from pyglotaran_extras.deprecation import warn_deprecated
+from pyglotaran_extras.io.setup_case_study import setup_case_study
+
+__all__ = ["setup_case_study"]
+
+warn_deprecated(
+    deprecated_qual_name_usage="pyglotaran_extras.io.boilerplate",
+    new_qual_name_usage="pyglotaran_extras.io",
+    to_be_removed_in_version="0.7.0",
+    stacklevel=3,
+)