Merge pull request #88 from loucerac/develop

Develop
loucerac · Jun 22, 2024 · f9bac0c · f9bac0c
2 parents 2fff673 + b76de49
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diff --git a/NES_FMdrug_targets.tsv b/NES_FMdrug_targets.tsv
diff --git a/README.md b/README.md
@@ -11,9 +11,9 @@ Repository for the `drexml` python package: (DRExM³L) Drug REpurposing using eX
 
 Find the associated publication [here](https://doi.org/10.1016/j.csbj.2024.02.027):
 
-```
+
 Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Computational and Structural Biotechnology Journal 2024;23:1129–43. https://doi.org/10.1016/j.csbj.2024.02.027.
-```
+
 
 Part of the [Intelligent Biology and Medicine](https://www.sciencedirect.com/science/journal/20010370/vsi/10XRHM1G1LS) special issue:
 
@@ -23,15 +23,18 @@ https://www.sciencedirect.com/journal/computational-and-structural-biotechnology
 And the `BIB` file:
 
 ```
-@article{ESTEBANMEDINA20241129,
-title = {drexml: A command line tool and Python package for drug repurposing},
-journal = {Computational and Structural Biotechnology Journal},
-volume = {23},
-pages = {1129-1143},
-year = {2024},
-issn = {2001-0370},
-doi = {https://doi.org/10.1016/j.csbj.2024.02.027},
-url = {https://www.sciencedirect.com/science/article/pii/S2001037024000515}
+@article{EstebanMedina2024,
+  title = {drexml: A command line tool and Python package for drug repurposing},
+  volume = {23},
+  ISSN = {2001-0370},
+  url = {http://dx.doi.org/10.1016/j.csbj.2024.02.027},
+  DOI = {10.1016/j.csbj.2024.02.027},
+  journal = {Computational and Structural Biotechnology Journal},
+  publisher = {Elsevier BV},
+  author = {Esteban-Medina,  Marina and de la Oliva Roque,  Víctor Manuel and Herráiz-Gil,  Sara and Peña-Chilet,  María and Dopazo,  Joaquín and Loucera,  Carlos},
+  year = {2024},
+  month = dec,
+  pages = {1129–1143}
 }
 ```
 
@@ -149,7 +152,7 @@ The recommended setup is:
 - use `pipx` to install `nox`
 - run `pdm config venv.backend conda`
 - run `make`, if you want to use a CUDA enabled GPU, use `make gpu=1`
-- (Recommended): For GPU development, clear the cache using `pdm clean cache` first
+- (Recommended): For GPU development, clear the cache using `pdm cache clear` first
 
 ## Documentation
 

diff --git a/drexml.Rproj b/drexml.Rproj
diff --git a/noxfile.py b/noxfile.py
@@ -28,4 +28,4 @@ def tests(session):
             pdm_env["PDM_NO_BINARY"] = "shap"
 
     session.run("pdm", "install", "-vd", external=True, env=pdm_env)
-    session.run("pytest")
+    session.run("pdm", "run", "pytest", external=True, env=pdm_env)
diff --git a/pyproject.toml b/pyproject.toml
@@ -9,7 +9,7 @@ authors = [
 requires-python = ">=3.8,<3.11"
 dependencies = [
     "scikit-learn>=1.3.0",
-    "numpy>=1.24.4",
+    "numpy>=1.24.4,<2.0",
     "scipy>=1.10.1",
     "pandas>=2.0.3",
     "seaborn>=0.12.2",
@@ -21,7 +21,7 @@ dependencies = [
     "pystow>=0.5.0",
 ]
 name = "drexml"
-version = "1.1.1"
+version = "1.1.2"
 description = "(DRExM³L) Drug REpurposing using and eXplainable Machine Learning and Mechanistic Models of signal transduction\""
 readme = "README.md"
 
@@ -53,7 +53,12 @@ dev = [
 
 [tool.pytest.ini_options]
 minversion = "6.0"
-addopts = "--ff -ra -v"
+addopts = [
+    "--ff",
+    "-ra",
+    "-v",
+    "--import-mode=importlib",
+]
 python_functions = [
     "test_*",
 ]

diff --git a/tests/__init__.py b/tests/__init__.py
@@ -1,6 +0,0 @@
-import os
-import sys
-
-PROJECT_PATH = os.getcwd()
-SOURCE_PATH = os.path.join(PROJECT_PATH, "drexml")
-sys.path.append(SOURCE_PATH)