Merge pull request #227 from PEtab-dev/release_0.2.4

Release 0.2.4
PEtab-dev · Sep 18, 2023 · 9f22a6d · 9f22a6d
2 parents 52d8ab1 + 82d4b2d
commit 9f22a6d
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Showing 68 changed files with 6,042 additions and 3,936 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -9,5 +9,5 @@ exclude_lines =
     raise NotImplementedError
     if __name__ == .__main__.:
 ignore_errors = True
-omit = 
+omit =
     tests/*
diff --git a/.flake8 b/.flake8
@@ -1,8 +1,12 @@
 [flake8]
 
 extend-ignore =
+    # whitespace before ":", conflicts with black
+    E203
     F403
     F405
+    # line too long, conflicts with black in rare cases
+    E501
 exclude =
     build,
     dist,

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,28 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-merge-conflict
+  - id: check-yaml
+    args: [--allow-multiple-documents]
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+    - id: black-jupyter
+      # It is recommended to specify the latest version of Python
+      # supported by your project here, or alternatively use
+      # pre-commit's default_language_version, see
+      # https://pre-commit.com/#top_level-default_language_version
+      language_version: python3.11
+      args: ["--line-length", "79"]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,19 @@
 
 ## 0.2 series
 
+### 0.2.4
+
+* Made figure sizes for visualization functions customizable via `petab.visualize.plotting.DEFAULT_FIGSIZE`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/222
+* Fixed Handling missing `nominalValue` in `Problem.get_x_nominal`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/223
+* Fixed pandas 2.1.0 `FutureWarnings`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/226
+* Added pre-commit-config, ran black, isort, ...
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/225
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.2.3...v0.2.4
+
 ### 0.2.3
 
 * Fixed validation failures in case of missing optional fields in visualization tables

diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@ The PEtab library is available on [pypi](https://pypi.org/project/petab/)
 and the easiest way to install it is running
 
     pip3 install petab
-    
+
 It will require Python>=3.9 to run. (We are following the
 [numpy Python support policy](https://numpy.org/neps/nep-0029-deprecation_policy.html)).
 
@@ -40,7 +40,7 @@ be:
     `petablint`
 
   - [`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, 
+    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)

diff --git a/doc/conf.py b/doc/conf.py
@@ -15,80 +15,80 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath(".."))
 
 # -- Project information -----------------------------------------------------
 
-project = 'libpetab-python'
-copyright = '2018, the PEtab developers'
-author = 'PEtab developers'
+project = "libpetab-python"
+copyright = "2018-2023, the PEtab developers"
+author = "PEtab developers"
 
 # The full version, including alpha/beta/rc tags
-release = 'latest'
+release = "latest"
 
 # -- Custom pre-build --------------------------------------------------------
 
 
-subprocess.run(['python', 'md2rst.py'])
+subprocess.run(["python", "md2rst.py"])
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'sphinx_markdown_tables',
-    'myst_nb',
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx_markdown_tables",
+    "myst_nb",
 ]
 
 intersphinx_mapping = {
-    'pandas': ('https://pandas.pydata.org/docs/', None),
-    'numpy': ('https://numpy.org/devdocs/', None),
-    'sympy': ('https://docs.sympy.org/latest/', None),
-    'python': ('https://docs.python.org/3', None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "numpy": ("https://numpy.org/devdocs/", None),
+    "sympy": ("https://docs.sympy.org/latest/", None),
+    "python": ("https://docs.python.org/3", None),
 }
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    'build/doctrees',
-    'build/html',
-    '**.ipynb_checkpoints',
-    'logo/LICENSE.md',
+    "build/doctrees",
+    "build/html",
+    "**.ipynb_checkpoints",
+    "logo/LICENSE.md",
 ]
 
-master_doc = 'index'
+master_doc = "index"
 
 autosummary_generate = True
 
 autodoc_default_options = {
     "members": None,
-    "imported-members": ['petab'],
+    "imported-members": ["petab"],
     "inherited-members": None,
     "private-members": None,
     "show-inheritance": None,
 }
 
 # For some reason causes sphinx import errors otherwise
-autodoc_mock_imports = ['yaml']
+autodoc_mock_imports = ["yaml"]
 
 # myst_nb options
 #  https://myst-nb.readthedocs.io/en/latest/configuration.html
 nb_execution_mode = "force"
 
 
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.txt': 'restructuredtext',
+    ".rst": "restructuredtext",
+    ".txt": "restructuredtext",
 }
 
 # ignore numpy warnings
@@ -100,12 +100,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 html_context = {
     "display_github": True,
@@ -115,15 +115,15 @@
     "conf_py_path": "/doc",
 }
 
-html_logo = 'logo/PEtab.png'
+html_logo = "logo/PEtab.png"
 
 
 def skip_some_objects(app, what, name, obj, skip, options):
     """Exclude some objects from the documentation"""
-    if getattr(obj, '__module__', None) == 'collections':
+    if getattr(obj, "__module__", None) == "collections":
         return True
 
 
 def setup(app):
     """Sphinx setup"""
-    app.connect('autodoc-skip-member', skip_some_objects)
+    app.connect("autodoc-skip-member", skip_some_objects)
diff --git a/doc/example/example_Fujita/Fujita_measurementData.tsv b/doc/example/example_Fujita/Fujita_measurementData.tsv
@@ -142,4 +142,4 @@ pS6_tot		model1_data6	0.07993	300	scaling_pS6_tot	0.01	model1_data6_pS6_tot
 pS6_tot		model1_data6	0.42868	600	scaling_pS6_tot	0.02	model1_data6_pS6_tot
 pS6_tot		model1_data6	0.60508	900	scaling_pS6_tot	0.03	model1_data6_pS6_tot
 pS6_tot		model1_data6	0.62088	1800	scaling_pS6_tot	0.035	model1_data6_pS6_tot
-pS6_tot		model1_data6	0.32084	3600	scaling_pS6_tot	0.07	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.32084	3600	scaling_pS6_tot	0.07	model1_data6_pS6_tot
diff --git a/doc/example/example_Fujita/Fujita_parameters_scaling.tsv b/doc/example/example_Fujita/Fujita_parameters_scaling.tsv
@@ -7,14 +7,14 @@ reaction_1_k1	reaction_{1,k1}	log10	1E-08	100000000	0.003690766129111	1	paramete
 reaction_1_k2	reaction_{1,k2}	log10	1E-08	100000000	0.002301175486005	1	laplace	1000;20	laplace	1000;20
 reaction_2_k1	reaction_{2,k1}	log10	1E-08	100000000	0.000936500808211	1	logLaplace	2;1	logLaplace	2;1
 reaction_2_k2	reaction_{2,k2}	log10	1E-08	100000000	60965.2066642586	1	parameterScaleLaplace	2;1	parameterScaleLaplace	2;1
-reaction_3_k1	reaction_{3,k1}	log10	1E-08	100000000	0.433225051651771	1				
-reaction_4_k1	reaction_{4,k1}	log10	1E-08	100000000	0.030155177423024	1				
-reaction_5_k1	reaction_{5,k1}	log10	1E-08	100000000	3.27310803801897E-06	1				
-reaction_5_k2	reaction_{5,k2}	log10	1E-08	100000000	0.000398546299782	1				
-reaction_6_k1	reaction_{6,k1}	log10	1E-08	100000000	5.46319692934546E-06	1				
-reaction_7_k1	reaction_{7,k1}	log10	1E-08	100000000	0.011803208311735	1				
-reaction_8_k1	reaction_{8,k1}	log10	1E-08	100000000	0.000944761775113	1				
-reaction_9_k1	reaction_{9,k1}	log10	1E-08	100000000	0.028510798479438	1				
-scaling_pAkt_tot	scaling_{pAkt}_tot	log10	1E-08	100000000	41.377103160384	1				
-scaling_pEGFR_tot	scaling_{pEGFR}_tot	log10	1E-08	100000000	5.64785460492811E-08	1				
-scaling_pS6_tot	scaling_{pS6}_tot	log10	1E-08	100000000	78521.9513232784	1				
+reaction_3_k1	reaction_{3,k1}	log10	1E-08	100000000	0.433225051651771	1
+reaction_4_k1	reaction_{4,k1}	log10	1E-08	100000000	0.030155177423024	1
+reaction_5_k1	reaction_{5,k1}	log10	1E-08	100000000	3.27310803801897E-06	1
+reaction_5_k2	reaction_{5,k2}	log10	1E-08	100000000	0.000398546299782	1
+reaction_6_k1	reaction_{6,k1}	log10	1E-08	100000000	5.46319692934546E-06	1
+reaction_7_k1	reaction_{7,k1}	log10	1E-08	100000000	0.011803208311735	1
+reaction_8_k1	reaction_{8,k1}	log10	1E-08	100000000	0.000944761775113	1
+reaction_9_k1	reaction_{9,k1}	log10	1E-08	100000000	0.028510798479438	1
+scaling_pAkt_tot	scaling_{pAkt}_tot	log10	1E-08	100000000	41.377103160384	1
+scaling_pEGFR_tot	scaling_{pEGFR}_tot	log10	1E-08	100000000	5.64785460492811E-08	1
+scaling_pS6_tot	scaling_{pS6}_tot	log10	1E-08	100000000	78521.9513232784	1
diff --git a/doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_empty.tsv b/doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_empty.tsv
@@ -1 +0,0 @@
-

diff --git a/doc/example/example_Isensee/Isensee_experimentalCondition.tsv b/doc/example/example_Isensee/Isensee_experimentalCondition.tsv
@@ -119,4 +119,4 @@ JI09_160126_Drg449_444_CycNuc__Fsk10_and_IBMX100	Fsk(10)/IBMX(100)	0	10	0	100	0
 JI09_160126_Drg449_444_CycNuc__Sp8_Br_cAMPS_AM10	Sp8-Br-cAMPS-AM(10)	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0
 JI09_160201_Drg453-452_CycNuc__ctrl	ctrl	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
 JI09_160201_Drg453-452_CycNuc__Fsk	Fsk(10)	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Sp8-Br-cAMPS-AM(10)	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0
+JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Sp8-Br-cAMPS-AM(10)	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0
diff --git a/doc/example/example_Isensee/Isensee_measurementData.tsv b/doc/example/example_Isensee/Isensee_measurementData.tsv
@@ -685,4 +685,4 @@ Calpha_Microscopy	control	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	1711.76
 Calpha_Microscopy	control	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	1970.37755061332	15	s_Calpha_global;b_Calpha_global;rel_open;xi_rel_open	s_Calpha_global;rho_Calpha_Microscopy	lin	normal	JI09_160201_Drg453_452_CycNuc	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Drg453
 Calpha_Microscopy	control	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	1950.86994136962	30	s_Calpha_global;b_Calpha_global;rel_open;xi_rel_open	s_Calpha_global;rho_Calpha_Microscopy	lin	normal	JI09_160201_Drg453_452_CycNuc	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Drg453
 Calpha_Microscopy	control	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	2016.8833683752	60	s_Calpha_global;b_Calpha_global;rel_open;xi_rel_open	s_Calpha_global;rho_Calpha_Microscopy	lin	normal	JI09_160201_Drg453_452_CycNuc	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Drg453
-Calpha_Microscopy	control	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	1802.11729015102	120	s_Calpha_global;b_Calpha_global;rel_open;xi_rel_open	s_Calpha_global;rho_Calpha_Microscopy	lin	normal	JI09_160201_Drg453_452_CycNuc	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Drg453
+Calpha_Microscopy	control	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	1802.11729015102	120	s_Calpha_global;b_Calpha_global;rel_open;xi_rel_open	s_Calpha_global;rho_Calpha_Microscopy	lin	normal	JI09_160201_Drg453_452_CycNuc	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	Drg453