From 14d67b7a0c7d1c9c4105cf170557b46841c4dbfd Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Fri, 26 Apr 2019 12:03:52 +0200 Subject: [PATCH 1/3] support for uncertainties --- sbmlutils/tests/modelcreator/test_modelcreator.py | 1 - setup.py | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/sbmlutils/tests/modelcreator/test_modelcreator.py b/sbmlutils/tests/modelcreator/test_modelcreator.py index de02eda3f..03210be68 100644 --- a/sbmlutils/tests/modelcreator/test_modelcreator.py +++ b/sbmlutils/tests/modelcreator/test_modelcreator.py @@ -64,6 +64,5 @@ def test_create_distrib(): distrib_factory.create_distrib(tmp=True) -@pytest.mark.skip(reason="Uncertainty currently not supported in libsbml-5.18.0") def test_create_distrib(): distrib_factory.create_distrib(tmp=True) diff --git a/setup.py b/setup.py index 38ec1c29b..e6291597d 100644 --- a/setup.py +++ b/setup.py @@ -77,13 +77,13 @@ def read(*names, **kwargs): "pyexcel-xlsx>=0.5.7", # standards - "python-libsbml>=5.18.0", + "python-libsbml-experimental>=5.18.0", "phrasedml>=1.0.9", # not working on py37 "antimony>=2.9.4", # not working on py37 # simulation "libroadrunner>=1.5.3", - # "cobra @ git+ssh://git@github.com/opencobra/cobrapy@sbml-bugfixes", # libSBML 5.18.0 dependencies + # "cobra @ git+ssh://git@github.com/opencobra/cobrapy@sbml-bugfixes", "cobra>=0.15.2", "optlang>=1.4.4", From 8f3e68bd414c863f0c62ef8dd33f984fb640b699 Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Mon, 29 Apr 2019 10:47:52 +0200 Subject: [PATCH 2/3] update dependencies for libsbml --- README.md | 2 +- requirements.txt | 1 - sbmlutils/_version.py | 2 +- .../distrib/{distrib_all.xml => distrib.xml} | 0 sbmlutils/distrib/uncertainty.xml | 1 - .../distrib/uncertainty_uncert_parameter.xml | 72 ------------------- sbmlutils/distrib/uncertainty_uncertspan.xml | 12 ---- sbmlutils/distrib/uncertainty_uncertvalue.xml | 21 ------ setup.py | 3 +- 9 files changed, 3 insertions(+), 111 deletions(-) delete mode 100644 requirements.txt rename sbmlutils/distrib/{distrib_all.xml => distrib.xml} (100%) delete mode 100644 sbmlutils/distrib/uncertainty_uncert_parameter.xml delete mode 100644 sbmlutils/distrib/uncertainty_uncertspan.xml delete mode 100644 sbmlutils/distrib/uncertainty_uncertvalue.xml diff --git a/README.md b/README.md index 4470abfa0..320993213 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ pip install -e . ``` ## Release notes -### 0.3.1 +### 0.3.1 - 0.3.3 * libSBML 5.18.0 * initial distrib support diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 9c558e357..000000000 --- a/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -. diff --git a/sbmlutils/_version.py b/sbmlutils/_version.py index 4cc71bf3f..8123e33e4 100644 --- a/sbmlutils/_version.py +++ b/sbmlutils/_version.py @@ -1,7 +1,7 @@ """ Definition of version string. """ -__version__ = "0.3.2" +__version__ = "0.3.3" PROGRAM_VERSION = __version__ PROGRAM_NAME = 'sbmlutils' diff --git a/sbmlutils/distrib/distrib_all.xml b/sbmlutils/distrib/distrib.xml similarity index 100% rename from sbmlutils/distrib/distrib_all.xml rename to sbmlutils/distrib/distrib.xml diff --git a/sbmlutils/distrib/uncertainty.xml b/sbmlutils/distrib/uncertainty.xml index 9008b1243..818bb83a9 100644 --- a/sbmlutils/distrib/uncertainty.xml +++ b/sbmlutils/distrib/uncertainty.xml @@ -4,7 +4,6 @@ - diff --git a/sbmlutils/distrib/uncertainty_uncert_parameter.xml b/sbmlutils/distrib/uncertainty_uncert_parameter.xml deleted file mode 100644 index f1ccf7159..000000000 --- a/sbmlutils/distrib/uncertainty_uncert_parameter.xml +++ /dev/null @@ -1,72 +0,0 @@ - - - - - - - - - -

Experimental data from study

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 5 - - normal - 1 - 3 - - - - - - - - - - - - - - - - - - - - diff --git a/sbmlutils/distrib/uncertainty_uncertspan.xml b/sbmlutils/distrib/uncertainty_uncertspan.xml deleted file mode 100644 index 0e72abf3c..000000000 --- a/sbmlutils/distrib/uncertainty_uncertspan.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff --git a/sbmlutils/distrib/uncertainty_uncertvalue.xml b/sbmlutils/distrib/uncertainty_uncertvalue.xml deleted file mode 100644 index e830885f8..000000000 --- a/sbmlutils/distrib/uncertainty_uncertvalue.xml +++ /dev/null @@ -1,21 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - diff --git a/setup.py b/setup.py index e6291597d..01e25ba35 100644 --- a/setup.py +++ b/setup.py @@ -83,8 +83,7 @@ def read(*names, **kwargs): # simulation "libroadrunner>=1.5.3", - # "cobra @ git+ssh://git@github.com/opencobra/cobrapy@sbml-bugfixes", - "cobra>=0.15.2", + "cobra>=0.15.3", "optlang>=1.4.4", # misc From 336fae978d0675b2e4ea37b58e19ff4ed5ea6d7f Mon Sep 17 00:00:00 2001 From: Matthias Koenig Date: Mon, 29 Apr 2019 10:54:21 +0200 Subject: [PATCH 3/3] fix missing requirements.txt --- requirements.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 000000000..945c9b46d --- /dev/null +++ b/requirements.txt @@ -0,0 +1 @@ +. \ No newline at end of file