Merge pull request #144 from Fxe/dev

Fix RAST parsing

.github/workflows/pre-commit.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v3

.github/workflows/tox.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python

.travis.yml

@@ -1,8 +1,8 @@
 language: python
 python:
-  - 3.7
-  - 3.8
   - 3.9
+  - 3.10
+  - 3.11
 before_install:
   - python --version
   - pip install -U pip

modelseedpy/core/msbuilder.py

@@ -1059,6 +1059,8 @@ def build_full_template_model(template, model_id=None, index="0"):
         :param index: index for the metabolites
         :return:
         """
+        from modelseedpy.core.msmodel import MSModel
+
         model = MSModel(model_id if model_id else template.id, template=template)
         all_reactions = []
         for rxn in template.reactions:

modelseedpy/core/msmodel.py

@@ -113,7 +113,6 @@ def get_set_set(expr_str):  # !!! this currently returns dictionaries, not sets?
         return {frozenset({str(x) for x in dnf.inputs})}
     else:
         return {frozenset({str(x) for x in o.inputs}) for o in dnf.xs}
-    return {}
 
 
 class MSModel(Model):

modelseedpy/core/rast_client.py

@@ -70,7 +70,7 @@ def annotate_genome(self, genome):
         for o in res[0]["features"]:
             feature = genome.features.get_by_id(o["id"])
             if "function" in o:
-                functions = re.split("; | / | @ | => ", o["function"])
+                functions = re.split("; | / | @", o["function"])
                 for function in functions:
                     feature.add_ontology_term("RAST", function)
 

setup.py

@@ -27,15 +27,14 @@
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Intended Audience :: Science/Research",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Natural Language :: English",
     ],
     install_requires=[
         "networkx >= 2.4",
-        "cobra >= 0.28.0",
+        "cobra >= 0.29.0",
         "scikit-learn == 1.2.0",  # version lock for pickle ML models
         "scipy >= 1.5.4",
         "chemicals >= 1.0.13",

tests/test_data/mock_data.py

@@ -271,10 +271,9 @@ def remap(model, bigg_to_seed_cpd, bigg_to_seed_rxn, index="0"):
 
 
 def mock_model_ecoli_core(seed=True):
-    from cobra.io import load_json_model
-    from os import path
+    from cobra.io import load_model
 
-    model = load_json_model(path.join(path.dirname(__file__), "e_coli_core.json"))
+    model = load_model("textbook")
     if not seed:
         return model
     bigg_to_seed_cpd = {

tox.ini

@@ -1,11 +1,11 @@
 [tox]
-envlist = py38,py39,py310
+envlist = py39,py310,py311
 
 [gh-actions]
 python =
-    3.8: py38
     3.9: py39
     3.10: py310
+    3.11: py311
 
 [testenv]
 setenv = ARCHIVEINTERFACE_CPCONFIG = {toxinidir}/server.conf