deprecate Python 3.7 support

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,4 +38,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
-        * Python version _(eg. 3.7, 3.8)_
+        * Python version _(eg. 3.10, 3.11)_

.github/workflows/create-test-wf.yml

@@ -29,10 +29,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/pytest.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3

.github/workflows/tools-api-docs-dev.yml

@@ -22,10 +22,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

.github/workflows/tools-api-docs-release.yml

@@ -21,10 +21,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install python dependencies
         run: |

CHANGELOG.md

@@ -44,6 +44,7 @@
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
 - Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
 - Handle `json.load()` exceptions ([#2134](https://github.com/nf-core/tools/pull/2134))
+- Deprecate Python 3.7 support because it reaches EOL
 
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 

nf_core/modules/test_yml_builder.py

@@ -213,16 +213,9 @@ def check_if_empty_file(self, fname):
                 g_f = gzip.GzipFile(fileobj=fh, mode="rb")
                 if g_f.read() == b"":
                     return True
-        except Exception as e:
-            # Python 3.8+
-            if hasattr(gzip, "BadGzipFile"):
-                if isinstance(e, gzip.BadGzipFile):
-                    pass
-            # Python 3.7
-            elif isinstance(e, OSError):
-                pass
-            else:
-                raise e
+        except gzip.BadGzipFile:
+            pass
+
         return False
 
     def _md5(self, fname):

nf_core/subworkflows/test_yml_builder.py

@@ -230,16 +230,9 @@ def check_if_empty_file(self, fname):
                 g_f = gzip.GzipFile(fileobj=fh, mode="rb")
                 if g_f.read() == b"":
                     return True
-        except Exception as e:
-            # Python 3.8+
-            if hasattr(gzip, "BadGzipFile"):
-                if isinstance(e, gzip.BadGzipFile):
-                    pass
-            # Python 3.7
-            elif isinstance(e, OSError):
-                pass
-            else:
-                raise e
+        except gzip.BadGzipFile:
+            pass
+
         return False
 
     def _md5(self, fname):

setup.py

@@ -35,7 +35,7 @@
         "console_scripts": ["nf-core=nf_core.__main__:run_nf_core"],
         "refgenie.hooks.post_update": ["nf-core-refgenie=nf_core.refgenie:update_config"],
     },
-    python_requires=">=3.7, <4",
+    python_requires=">=3.8, <4",
     install_requires=required,
     packages=find_packages(exclude=("docs")),
     include_package_data=True,