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Deprecate Python 3.7 support #2210

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Merged
fabianegli merged 3 commits into from
Mar 27, 2023
Merged

Deprecate Python 3.7 support #2210

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92238f1
deprecate Python 3.7 support
fabianegli Mar 27, 2023
2505810
add link to PR
fabianegli Mar 27, 2023
68e011b
Merge branch 'dev' into deprecate-Python-3.7-support
fabianegli Mar 27, 2023
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -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)_
4 changes: 2 additions & 2 deletions .github/workflows/create-test-wf.yml
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Expand Up @@ -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: |
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4 changes: 2 additions & 2 deletions .github/workflows/deploy-pypi.yml
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Expand Up @@ -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: |
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2 changes: 1 addition & 1 deletion .github/workflows/pytest.yml
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions .github/workflows/tools-api-docs-dev.yml
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Expand Up @@ -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: |
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4 changes: 2 additions & 2 deletions .github/workflows/tools-api-docs-release.yml
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Expand Up @@ -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: |
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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 ([#2210](https://github.com/nf-core/tools/pull/2210))

## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]

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13 changes: 3 additions & 10 deletions nf_core/modules/test_yml_builder.py
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Expand Up @@ -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):
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13 changes: 3 additions & 10 deletions nf_core/subworkflows/test_yml_builder.py
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Expand Up @@ -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):
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -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,
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