Merge pull request #201 from PEtab-dev/release_0.2.0

Release 0.2.0
PEtab-dev · May 8, 2023 · 3c29fa1 · 3c29fa1
2 parents 2ba5c52 + 9fbf14c
commit 3c29fa1
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Showing 45 changed files with 1,883 additions and 196 deletions.
diff --git a/.flake8 b/.flake8
@@ -4,11 +4,12 @@ extend-ignore =
     F403
     F405
 exclude =
-    build
-    dist
-    doc
-    env
-    venv
-    example
-    tmp
-    _*
+    build,
+    dist,
+    doc,
+    env,
+    venv,
+    example,
+    tmp,
+    _*,
+    .tox,
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -0,0 +1,12 @@
+# see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+# default owners
+* @PEtab-dev/libpetab-python-maintainers
+
+/petab/visualize/ @plakrisenko
+/tests/test_vis* @plakrisenko
+/petab/simulate.py @dilpath
+/tests/test_simulate.py @dilpath
+/petab/calculate.py @yannikschaelte
+/tests/test_calculate.py @yannikschaelte
+/doc/ @dweindl
diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -11,25 +11,26 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ["3.8", "3.10"]
+        python-version: ["3.9", "3.11"]
     runs-on: ${{ matrix.platform }}
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Get pip cache directory
       id: pip_cache_dir
       run: |
-        echo "::set-output name=dir::$(pip cache dir)"
+        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+      shell: bash
 
     - name: Cache
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: ${{ steps.pip_cache_dir.outputs.dir }}
         key: ${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/.ci_pip_reqs.txt') }}-${{ hashFiles('**/setup.py') }}
@@ -49,7 +50,7 @@ jobs:
       run: tox -e unit
 
     - name: Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -10,11 +10,11 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,11 +7,15 @@ sphinx:
    configuration: doc/conf.py
    fail_on_warning: true
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
 
 python:
-   version: 3.8
    install:
    - method: pip
      path: .
      extra_requirements:
         - doc
+        - vis
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,41 @@
 # PEtab changelog
 
+## 0.2 series
+
+### 0.2.0
+
+Note: petab 0.2.0 requires Python>=3.9
+
+Features:
+* Plot measurements for t = 'inf'
+  by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/149
+* Added validation for visualization files
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/184
+  https://github.com/PEtab-dev/libpetab-python/pull/189
+* Startpoints as dict
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/188
+* Residuals plot
+  by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/187
+  https://github.com/PEtab-dev/libpetab-python/pull/191
+* add goodness of fit plot
+  by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/192
+* Add PySBModel for handling of PySB models
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/145
+
+Fixes
+* Vis: Don't fail on missing simulations
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/185
+* prevent strings being parsed as nan in get_visualization_df
+  by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/193
+* Fix get_model_for_condition
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/194
+* Simulator: rename measurement column to simulation
+  by @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/199
+* Fix sympy symbol name clashes
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/202
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.1.30...v0.2.0
+
 ## 0.1 series
 
 ### 0.1.30

diff --git a/doc/example/example_Fujita/Fujita_measurementData_t_inf.tsv b/doc/example/example_Fujita/Fujita_measurementData_t_inf.tsv
@@ -0,0 +1,57 @@
+observableId	preequilibrationConditionId	simulationConditionId	measurement	time	observableParameters	noiseParameters	datasetId
+pS6_tot		model1_data1	0	0	scaling_pS6_tot	0.01	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.0018563	60	scaling_pS6_tot	0.01	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.0033416	120	scaling_pS6_tot	0.01	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.012632	300	scaling_pS6_tot	0.01	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.078914	600	scaling_pS6_tot	0.02	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.25521	900	scaling_pS6_tot	0.02	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.44745	1800	scaling_pS6_tot	0.035	model1_data1_pS6_tot
+pS6_tot		model1_data1	0.29547	inf	scaling_pS6_tot	0.035	model1_data1_pS6_tot
+pS6_tot		model1_data2	0	0	scaling_pS6_tot	0.01	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.0019654	60	scaling_pS6_tot	0.01	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.0021975	120	scaling_pS6_tot	0.01	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.020119	300	scaling_pS6_tot	0.01	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.22158	600	scaling_pS6_tot	0.02	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.52331	900	scaling_pS6_tot	0.03	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.85846	1800	scaling_pS6_tot	0.1	model1_data2_pS6_tot
+pS6_tot		model1_data2	0.6598	inf	scaling_pS6_tot	0.025	model1_data2_pS6_tot
+pS6_tot		model1_data3	0	0	scaling_pS6_tot	0.01	model1_data3_pS6_tot
+pS6_tot		model1_data3	0.0020839	60	scaling_pS6_tot	0.01	model1_data3_pS6_tot
+pS6_tot		model1_data3	0.0047955	120	scaling_pS6_tot	0.01	model1_data3_pS6_tot
+pS6_tot		model1_data3	0.047495	300	scaling_pS6_tot	0.01	model1_data3_pS6_tot
+pS6_tot		model1_data3	0.39197	600	scaling_pS6_tot	0.01	model1_data3_pS6_tot
+pS6_tot		model1_data3	0.68142	900	scaling_pS6_tot	0.025	model1_data3_pS6_tot
+pS6_tot		model1_data3	1.0001	1800	scaling_pS6_tot	0.07	model1_data3_pS6_tot
+pS6_tot		model1_data3	0.75108	inf	scaling_pS6_tot	0.075	model1_data3_pS6_tot
+pS6_tot		model1_data4	0	0	scaling_pS6_tot	0.01	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.0057189	60	scaling_pS6_tot	0.01	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.013126	120	scaling_pS6_tot	0.01	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.062408	300	scaling_pS6_tot	0.01	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.41154	600	scaling_pS6_tot	0.01	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.71428	900	scaling_pS6_tot	0.035	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.92784	1800	scaling_pS6_tot	0.08	model1_data4_pS6_tot
+pS6_tot		model1_data4	0.55064	inf	scaling_pS6_tot	0.08	model1_data4_pS6_tot
+pS6_tot		model1_data5	0	0	scaling_pS6_tot	0.01	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.0073292	60	scaling_pS6_tot	0.01	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.014418	120	scaling_pS6_tot	0.01	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.079732	300	scaling_pS6_tot	0.01	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.4562	600	scaling_pS6_tot	0.01	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.65294	900	scaling_pS6_tot	0.02	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.75189	1800	scaling_pS6_tot	0.04	model1_data5_pS6_tot
+pS6_tot		model1_data5	0.37446	inf	scaling_pS6_tot	0.08	model1_data5_pS6_tot
+pS6_tot		model1_data6	0	0	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.0086144	60	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.013062	120	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+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	inf	scaling_pS6_tot	0.07	model1_data6_pS6_tot
+pS6_tot		model1_data6	0	0	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.009	60	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.01	120	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.05	300	scaling_pS6_tot	0.01	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.6	600	scaling_pS6_tot	0.02	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.4	900	scaling_pS6_tot	0.03	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.83	1800	scaling_pS6_tot	0.035	model1_data6_pS6_tot
+pS6_tot		model1_data6	0.2	inf	scaling_pS6_tot	0.07	model1_data6_pS6_tot
diff --git a/doc/example/example_Fujita/Fujita_simulatedData_t_inf.tsv b/doc/example/example_Fujita/Fujita_simulatedData_t_inf.tsv
@@ -0,0 +1,49 @@
+observableId	preequilibrationConditionId	simulationConditionId	simulation	time	observableParameters	noiseParameters
+pS6_tot		model1_data1	0	0	scaling_pS6_tot	0.01
+pS6_tot		model1_data1	5.78895984805857E-05	60	scaling_pS6_tot	0.01
+pS6_tot		model1_data1	0.0009531255	120	scaling_pS6_tot	0.01
+pS6_tot		model1_data1	0.0185497283	300	scaling_pS6_tot	0.01
+pS6_tot		model1_data1	0.0927501675	600	scaling_pS6_tot	0.02
+pS6_tot		model1_data1	0.1859892615	900	scaling_pS6_tot	0.02
+pS6_tot		model1_data1	0.3842285889	1800	scaling_pS6_tot	0.035
+pS6_tot		model1_data1	0.3671651134	inf	scaling_pS6_tot	0.035
+pS6_tot		model1_data2	0	0	scaling_pS6_tot	0.01
+pS6_tot		model1_data2	0.0001694707	60	scaling_pS6_tot	0.01
+pS6_tot		model1_data2	0.0026563935	120	scaling_pS6_tot	0.01
+pS6_tot		model1_data2	0.045833771	300	scaling_pS6_tot	0.01
+pS6_tot		model1_data2	0.209607514	600	scaling_pS6_tot	0.02
+pS6_tot		model1_data2	0.4007484657	900	scaling_pS6_tot	0.03
+pS6_tot		model1_data2	0.7556316274	1800	scaling_pS6_tot	0.1
+pS6_tot		model1_data2	0.6612775029	inf	scaling_pS6_tot	0.025
+pS6_tot		model1_data3	0	0	scaling_pS6_tot	0.01
+pS6_tot		model1_data3	0.0005211244	60	scaling_pS6_tot	0.01
+pS6_tot		model1_data3	0.007106942	120	scaling_pS6_tot	0.01
+pS6_tot		model1_data3	0.0945320284	300	scaling_pS6_tot	0.01
+pS6_tot		model1_data3	0.366852041	600	scaling_pS6_tot	0.01
+pS6_tot		model1_data3	0.6350909024	900	scaling_pS6_tot	0.025
+pS6_tot		model1_data3	0.9989387811	1800	scaling_pS6_tot	0.07
+pS6_tot		model1_data3	0.7818807584	inf	scaling_pS6_tot	0.075
+pS6_tot		model1_data4	0	0	scaling_pS6_tot	0.01
+pS6_tot		model1_data4	0.001284326	60	scaling_pS6_tot	0.01
+pS6_tot		model1_data4	0.0137701475	120	scaling_pS6_tot	0.01
+pS6_tot		model1_data4	0.1357831768	300	scaling_pS6_tot	0.01
+pS6_tot		model1_data4	0.4317319675	600	scaling_pS6_tot	0.01
+pS6_tot		model1_data4	0.6581119566	900	scaling_pS6_tot	0.035
+pS6_tot		model1_data4	0.8936164338	1800	scaling_pS6_tot	0.08
+pS6_tot		model1_data4	0.6665565723	inf	scaling_pS6_tot	0.08
+pS6_tot		model1_data5	0	0	scaling_pS6_tot	0.01
+pS6_tot		model1_data5	0.0026774961	60	scaling_pS6_tot	0.01
+pS6_tot		model1_data5	0.0210783997	120	scaling_pS6_tot	0.01
+pS6_tot		model1_data5	0.1570157565	300	scaling_pS6_tot	0.01
+pS6_tot		model1_data5	0.4117751573	600	scaling_pS6_tot	0.01
+pS6_tot		model1_data5	0.5823970015	900	scaling_pS6_tot	0.02
+pS6_tot		model1_data5	0.7468131737	1800	scaling_pS6_tot	0.04
+pS6_tot		model1_data5	0.5504628923	inf	scaling_pS6_tot	0.08
+pS6_tot		model1_data6	0	0	scaling_pS6_tot	0.01
+pS6_tot		model1_data6	0.0039799398	60	scaling_pS6_tot	0.01
+pS6_tot		model1_data6	0.0254606658	120	scaling_pS6_tot	0.01
+pS6_tot		model1_data6	0.1631478226	300	scaling_pS6_tot	0.01
+pS6_tot		model1_data6	0.4009703836	600	scaling_pS6_tot	0.02
+pS6_tot		model1_data6	0.5574326493	900	scaling_pS6_tot	0.03
+pS6_tot		model1_data6	0.7058108511	1800	scaling_pS6_tot	0.035
+pS6_tot		model1_data6	0.5194180219	inf	scaling_pS6_tot	0.07
diff --git a/doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_replicates.tsv b/doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_replicates.tsv
@@ -0,0 +1,2 @@
+plotId	xValues	yValues	yOffset	yScale	plotName	plotTypeSimulation	plotTypeData
+plot1	time	pS6_tot	0	lin	pS6 total	LinePlot	replicate
diff --git a/petab/C.py b/petab/C.py
@@ -234,6 +234,12 @@
 #: Supported plot types
 PLOT_TYPES_SIMULATION = [LINE_PLOT, BAR_PLOT, SCATTER_PLOT]
 
+#: Supported xScales
+X_SCALES = [LIN, LOG, LOG10]
+
+#: Supported yScales
+Y_SCALES = [LIN, LOG, LOG10]
+
 
 #:
 MEAN_AND_SD = 'MeanAndSD'
@@ -257,6 +263,12 @@
 #:
 SBML_FILES = 'sbml_files'
 #:
+MODEL_FILES = 'model_files'
+#:
+MODEL_LOCATION = 'location'
+#:
+MODEL_LANGUAGE = 'language'
+#:
 CONDITION_FILES = 'condition_files'
 #:
 MEASUREMENT_FILES = 'measurement_files'
@@ -265,9 +277,19 @@
 #:
 VISUALIZATION_FILES = 'visualization_files'
 #:
+MAPPING_FILES = 'mapping_files'
+#:
 EXTENSIONS = 'extensions'
 
 
+# MAPPING
+#:
+PETAB_ENTITY_ID = 'petabEntityId'
+#:
+MODEL_ENTITY_ID = 'modelEntityId'
+#:
+MAPPING_DF_REQUIRED_COLS = [PETAB_ENTITY_ID, MODEL_ENTITY_ID]
+
 # MORE
 
 #:

diff --git a/petab/__init__.py b/petab/__init__.py
@@ -28,3 +28,4 @@
 from .yaml import *  # noqa: F403, F401, E402
 from .version import __version__  # noqa: F401, E402
 from .format_version import __format_version__  # noqa: F401, E402
+from .mapping import *  # noqa: F403, F401, E402
diff --git a/petab/calculate.py b/petab/calculate.py
@@ -6,9 +6,10 @@
 
 import numpy as np
 import pandas as pd
-import petab
 import sympy
+from sympy.abc import _clash
 
+import petab
 from .C import *
 
 __all__ = ['calculate_residuals', 'calculate_residuals_for_table',
@@ -138,7 +139,7 @@ def get_symbolic_noise_formulas(observable_df) -> Dict[str, sympy.Expr]:
         if NOISE_FORMULA not in observable_df.columns:
             noise_formula = None
         else:
-            noise_formula = sympy.sympify(row.noiseFormula)
+            noise_formula = sympy.sympify(row.noiseFormula, locals=_clash)
         noise_formulas[observable_id] = noise_formula
     return noise_formulas
 

diff --git a/petab/core.py b/petab/core.py
@@ -64,7 +64,9 @@ def get_visualization_df(visualization_file: Union[str, Path]) -> pd.DataFrame:
         Visualization DataFrame
     """
     try:
+        types = {PLOT_NAME: str}
         vis_spec = pd.read_csv(visualization_file, sep="\t", index_col=None,
+                               converters=types,
                                float_precision='round_trip')
     except pd.errors.EmptyDataError:
         warn("Visualization table is empty. Defaults will be used. "
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,11 +4,12 @@ extend-ignore = @@
         F403
         F405
     exclude =
-        build
-        dist
-        doc
-        env
-        venv
-        example
-        tmp
-        _*
+        build,
+        dist,
+        doc,
+        env,
+        venv,
+        example,
+        tmp,
+        _*,
+        .tox,
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		plotId xValues yValues yOffset yScale plotName plotTypeSimulation plotTypeData
		plot1 time pS6_tot 0 lin pS6 total LinePlot replicate