Remove deprecated pkg_resources (#352)

* Remove Removed depreacted pkg_resources

* Switch to python 3.9 in test

---------

Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>

Author: northwestwitch

.github/workflows/pytest_codecov.yml

@@ -13,10 +13,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install deps
         run: |
@@ -46,10 +46,10 @@ jobs:
 
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
         # Cache package installation step to speed up the following step
       - uses: actions/cache@v4
@@ -76,10 +76,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: Install deps
         run: |
           python -m pip install --upgrade pip

CHANGELOG.md

@@ -1,3 +1,7 @@
+## [unreleased]
+### Fixed
+- Removed depreacted pkg_resources
+
 ## [4.5.1] - 2024-09-04
 ### Fixed
 - Bump actions/download-artifact from 2 to 4 in /.github/workflows (recommended by security advisory)

patientMatcher/resources/__init__.py

@@ -1,4 +1,4 @@
-import pkg_resources
+from importlib.resources import files
 
 ###### Files ######
 hpo_filename = "resources/hp.obo.txt"
@@ -7,12 +7,9 @@
 json_api = "resources/api.json"
 
 ###### Paths ######
-path_to_hpo_terms = pkg_resources.resource_filename("patientMatcher", hpo_filename)
+base = files("patientMatcher")
 
-path_to_phenotype_annotations = pkg_resources.resource_filename(
-    "patientMatcher", phenotype_annotation_filename
-)
-
-path_to_benchmark_patients = pkg_resources.resource_filename("patientMatcher", benchmark_patients)
-
-path_to_json_api = pkg_resources.resource_filename("patientMatcher", json_api)
+path_to_hpo_terms = str(base.joinpath(hpo_filename))
+path_to_phenotype_annotations = str(base.joinpath(phenotype_annotation_filename))
+path_to_benchmark_patients = str(base.joinpath(benchmark_patients))
+path_to_json_api = str(base.joinpath(json_api))