use pandas map to simplify code plus some maintenance

🎨 applymap is depreceated since pandas 2.1

.github/workflows/ci.yml

@@ -13,13 +13,13 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       # Set up the specific Python version for Black
       - name: Set up Python 3.12
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.12  # Set your desired Python version here
+          python-version: "3.12"  # Set your desired Python version here
 
       # Install Black and dependencies if necessary
       - name: Install Black
@@ -52,26 +52,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: python-isort
-        uses: isort/isort-action@v0.1.0
+        uses: isort/isort-action@v1
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"
 
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/conda-build.yml

@@ -8,13 +8,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Miniconda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
-        python-version: 3.9
+        python-version: '3.10'
         channels: conda-forge,defaults,bioconda
 
     - name: Create conda environment

.github/workflows/pythonapp.yml

@@ -15,11 +15,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pythonpackage.yml

@@ -15,12 +15,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
-
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/pythonpublish.yml

@@ -23,7 +23,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

environment.yml

@@ -4,10 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=3.8
+  - python=3.10
   - conda-build
   - anaconda-client
-  - pandas
+  - pandas>=2.1
   - click
   - requests
   - pyyaml
@@ -17,4 +17,4 @@ dependencies:
   - python-duckdb
   - rdflib
   - pandas_schema
-
+  - setuptools

recipe/meta.yaml

@@ -16,20 +16,21 @@ build:
 requirements:
   host:
     - pip
-    - python >=3.5
+    - python >=3.10
     - setuptools
   run:
     - click
     - requests
     - pandas
     - pandas_schema
-    - python >=3.5
+    - python >=3.10
     - pyaml
     - defusedxml
     - pytest
     - duckdb
     - rdflib
     - pyarrow
+    - setuptools
 
 test:
   imports:
@@ -47,4 +48,4 @@ about:
   ##license_file: LICENSE ## patch is applied upstream, next version will have it
   summary: "Translate, convert SDRF to configuration pipelines"
   doc_url: "https://github.com/bigbio/sdrf-pipelines"
-  dev_url: "https://github.com/bigbio/sdrf-pipelines"
+  dev_url: "https://github.com/bigbio/sdrf-pipelines"

requirements.txt

@@ -1,4 +1,4 @@
-pandas
+pandas>2.1
 click
 # https://github.com/multimeric/PandasSchema does not seem to be maintained
 # anymore, and right now it thows a pandas deprecation warning, in the
@@ -12,4 +12,4 @@ defusedxml
 pyarrow
 duckdb
 rdflib
-setuptools
+setuptools

sdrf_pipelines/sdrf/sdrf_schema.py

@@ -361,12 +361,7 @@ def validate_empty_cells(self, panda_sdrf):
         def validate_string(cell_value):
             return cell_value is not None and cell_value != "nan" and len(cell_value.strip()) > 0
 
-        if sys.version_info <= (3, 8):
-            # Use map for Python versions less than 3.8
-            validation_results = panda_sdrf.map(validate_string)
-        else:
-            # Use applymap for Python versions 3.8 and above
-            validation_results = panda_sdrf.applymap(validate_string)
+        validation_results = panda_sdrf.map(validate_string)
 
         # Get the indices where the validation fails
         failed_indices = [