Add py312 support to template and drop pdm testing

pdm cannot resolve different dependency versions for different python versions, and there is no numpy version that can be simultaneously resolved both to python 3.8 and python 3.12. So the only way to use support pdm would be to raise the lower limit of our template app, or have special pdm support. Users can still use pdm if they wish, but they'll have to work out the consequences themselves. pdm is removed from printed instructions and testing
khanlab · Jan 11, 2024 · 9954f06 · 9954f06
1 parent be03774
commit 9954f06
Show file tree

Hide file tree

Showing 5 changed files with 54 additions and 74 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,9 +23,7 @@ style = "pep440"
 bump = true
 
 [tool.poetry-dynamic-versioning.substitution]
-files = [
-    'snakebids/__init__.py',
-]
+files = ['snakebids/__init__.py']
 patterns = [
     "(^\\s+\"snakebids_version\":\\s*\")[^'\"]*(\")",
     "(^__version__\\s*(?::.*?)?=\\s*['\"])[^'\"]*(['\"])",
@@ -66,7 +64,6 @@ scipy = [
 pandas = [
     { version = "<=2.0.3", python = "<3.9" },
     { version = ">=2.1.1", python = ">=3.12" },
-
 ]
 # minimum 8.2.0 to use post-copy mesages
 copier = ">=8.2.0"
@@ -132,8 +129,8 @@ expr = "platform.python_version()"
 args = [{ name = "container_id", positional = true, required = true }]
 uses = { VERSION = "_get_version" }
 cmd = """
-    docker build 'containers/${container_id}' \
-        --tag 'snakebids/${container_id}:${VERSION}' \
+    docker build "containers/${container_id}" \
+        --tag "snakebids/${container_id}:${VERSION}" \
         --build-arg="PYTHON_VERSION=${VERSION}"
 """
 
@@ -143,18 +140,15 @@ markers = [
 ]
 
 [tool.coverage.run]
-omit = [
-    "snakebids/project_template/**",
-    "snakebids/tests/**",
-]
+omit = ["snakebids/project_template/**", "snakebids/tests/**"]
 
 [tool.coverage.report]
 exclude_lines = [
     "pragma: not covered",
     "@overload",
     'class [a-zA-Z0-9_]+\([^)]*Protocol.*\)',
     'if TYPE_CHECKING',
-    "def __dir__"
+    "def __dir__",
 ]
 
 [tool.isort]
@@ -170,31 +164,31 @@ reportImportCycles = false
 
 [tool.ruff]
 select = [
-    "E",    # pycodestyle error
-    "W",    # pycodestyle warning
-    "F",    # pyflakes
-    "N",    # pep8-naming
-    "UP",   # pyupgrade
-    "YTT",  # flake8-2020
-    "S",    # flake8-bandit
-    "BLE",  # flake8-blind-except
-    "B",    # flake8-bugbear
-    "A",    # flake8-builtins
-    "COM",  # flake8-commas
-    "C4",   # flake8-comprehensions
-    "T10",  # flake8-debugger
-    "EM",   # flake8-errmsg
-    "FA",   # flake8-future-annotations
-    "ISC",  # flake8-implicit-str-concat
-    "ICN",  # flake8-import-conventions
-    "G",    # flake8-logging-format
-    "INP",  # flake8-no-pep420
-    "PIE",  # flake8-pie
-    "PT",   # flake8-pytest-style
-    "RSE",  # flake8-raise
-    "RET",  # flake8-return
-    "SLF",  # flake8-self
-    "SIM",  # flake8-simplify
+    "E",   # pycodestyle error
+    "W",   # pycodestyle warning
+    "F",   # pyflakes
+    "N",   # pep8-naming
+    "UP",  # pyupgrade
+    "YTT", # flake8-2020
+    "S",   # flake8-bandit
+    "BLE", # flake8-blind-except
+    "B",   # flake8-bugbear
+    "A",   # flake8-builtins
+    "COM", # flake8-commas
+    "C4",  # flake8-comprehensions
+    "T10", # flake8-debugger
+    "EM",  # flake8-errmsg
+    "FA",  # flake8-future-annotations
+    "ISC", # flake8-implicit-str-concat
+    "ICN", # flake8-import-conventions
+    "G",   # flake8-logging-format
+    "INP", # flake8-no-pep420
+    "PIE", # flake8-pie
+    "PT",  # flake8-pytest-style
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "SLF", # flake8-self
+    "SIM", # flake8-simplify
     # We use os.path a lot in "legitimate" ways, so this ruleset has too many
     # false positives
     # "PTH",  # flake8-use-pathlib
@@ -210,11 +204,11 @@ select = [
 ]
 ignore = [
     "PLR0913",
-    "D105",     # missing docstring in magic method
-    "D100",     # Require docstring in public modules
-    "D104",     # Require docstring in public packages
-    "S603",     # Subprocess without shell equals true
-    "S607",     # start-process-with-partial-path
+    "D105",    # missing docstring in magic method
+    "D100",    # Require docstring in public modules
+    "D104",    # Require docstring in public packages
+    "S603",    # Subprocess without shell equals true
+    "S607",    # start-process-with-partial-path
     # recommended ignores for ruff format
     "W191",
     "E111",
@@ -241,8 +235,8 @@ namespace-packages = ["snakebids/plugins"]
 "snakebids/project_template/**" = ["N999"]
 "snakebids/tests/**" = [
     "D",
-    "S101",     # assert
-    "S307",     # Use of eval
+    "S101", # assert
+    "S307", # Use of eval
     "SLF",
 ]
 

diff --git a/snakebids/project_template/copier.yaml b/snakebids/project_template/copier.yaml
@@ -65,7 +65,7 @@ bids_version:
   when: false
 
 python_version:
-  default: ">=3.8,<3.12"
+  default: ">=3.8,<3.13"
   when: false
 
 snakebids_version:
@@ -96,27 +96,16 @@ _message_after_copy: >
 
     $ cd {{ _copier_conf.dst_path }}
 
-  {% if build_system == "poetry" -%}
   {{ Fore.BLUE }}2.{{ Fore.RESET }} Install dependencies.
 
+  {% if build_system == "poetry" %}
     $ poetry install
-
-  {%- else -%}
-  {{ Fore.BLUE + "2." + Fore.RESET + """ Install dependencies. This may vary
-  depending on your tooling. The following are examples (the first example
-  should work on any python environment; the others require 3rd party tools):
-  """ | wordwrap(80)}}
-
-    * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}}
-      $ python -m venv .venv
-      $ source .venv/bin/activate
-      $ pip install .
-
-    * {{Fore.YELLOW}}Hatch:{{Fore.RESET}}
-      $ hatch env create
-
-    * {{Fore.YELLOW}}PDM:{{Fore.RESET}}
-      $ pdm install
+  {%- elif build_system == "hatch" %}
+    $ hatch env create
+  {%- else %}
+    $ python -m venv .venv
+    $ source .venv/bin/activate
+    $ pip install .
   {%- endif %}
 
 
@@ -125,15 +114,12 @@ _message_after_copy: >
   {% if build_system == "poetry" %}
     $ poetry run {{ test_run_cmd }}
 
-  {%- else %}
-    * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}}
-      $ {{ test_run_cmd }}
+  {%- elif build_system == "hatch" %}
+    $ hatch env run -- {{ test_run_cmd }}
 
-    * {{Fore.YELLOW}}Hatch:{{Fore.RESET}}
-      $ hatch env run -- {{ test_run_cmd }}
+  {%- else %}
+    $ {{ test_run_cmd }}
 
-    * {{Fore.YELLOW}}PDM:{{Fore.RESET}}
-      $ pdm run {{ test_run_cmd }}
   {%- endif %}
 
 _jinja_extensions:

diff --git a/snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja b/snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja
@@ -30,10 +30,6 @@ requires-python = "{{ python_version }}"
 dependencies = [
     "snakemake >= {{ snakemake_version }},<8",
     "snakebids >= {{ snakebids_version }}",
-    {# Explicitly specify numpy version for py38 until snakebids 0.10.x to
-       work around specification bug causing numpys too high for py38 to be
-       locked by pdm -#}
-    "numpy <=1.24.4; python_version < \"3.9\"",
 ]
 
 [project.scripts]

diff --git a/snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja b/snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja
@@ -24,6 +24,10 @@ classifiers = [
 python = "{{ python_version }}"
 snakemake = ">={{ snakemake_version }},<8"
 snakebids = ">={{ snakebids_version }}"
+pandas = [
+    { version = "<=2.0.3", python = "<3.9" },
+    { version = ">=2.1.1", python = ">=3.12" },
+]
 
 [tool.poetry.scripts]
 {{ name_slug }} = "{{ name_slug }}.run:main"

diff --git a/snakebids/tests/test_template.py b/snakebids/tests/test_template.py
@@ -270,7 +270,7 @@ def test_pyproject_correctly_formatted(
         ("setuptools", "setuptools"),
         ("poetry", "poetry"),
         ("hatch", "hatch"),
-        ("flit", "pdm"),
+        ("flit", "setuptools"),
     ],
 )
 def test_template_dry_runs_successfully(tmp_path: Path, build: BuildBackend, venv: str):