Merge development branch (#42)

* Fixing issues with CLI, adding to README, adding to CLI (#37)

* csv separator autodetection
* more integration tests via cli
* Adding proper help text to arguments
* adding Recon3D models and sequence data via Git LFS
* additional information on readme
* json model support for the CLI
* add option to only run fast tests
* flipping CLI argument order
* simplification, fixing tests

* adding .mat file support to CLI

* fix package version pinning (#41)

* fix pinning of package versions that wasn't working
* upgrade pylint as the old version crashed

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gemcat"
-version = "1.2.0"
+version = "1.2.1"
 
 description = "A toolbox for gene expression-based prediction of metabolic alterations"
 keywords = ["python", "bioinformatics", "modeling", "metabolites", "omics"]
@@ -15,22 +15,23 @@ readme = "README.md"
 
 requires-python=">=3.10"
 dependencies = [
-    "numpy>=1.26.2",
-    "pandas>=2.1.4",
-    "cobra>=0.29.0",
-    "networkx>=3.2.1",
-    "scipy>=1.11.4",
-    "sympy>=1.12",
+    "numpy==1.26.*",
+    "pandas==2.1.*",
+    "cobra==0.29.*",
+    "networkx==3.2.*",
+    "scipy==1.11.*",
+    "sympy==1.12.*",
 ]
 
 [project.optional-dependencies]
 dev = [
-  "pytest>=7.4.0",
-  "black>=23.7.0",
-  "isort>=5.12.0",
-  "pylint>=2.17.7",
-  "ruff>=0.0.292",
-  "requests>=2.31.0",
+  "pytest==7.4.*",
+  "black==23.7.*",
+  "isort==5.12.*",
+  "pylint==3.1.*",
+  "ruff==0.0.*",
+  "requests==2.31.*",
+
 ]
 
 [tool.setuptools.packages.find]