Add environment.yml support to the rest of FawltyDeps

Now that we can parse dependency declarations from environment.yml
files, we need to expose this functionality in our docs + CLI, as
well as automatically find environment.yml files while traversing
projects.

Author: jherland

README.md

@@ -130,6 +130,7 @@ dependencies. A number of file formats are supported:
   `extras_require` arguments)
 - `setup.cfg`
 - `pixi.toml`
+- `environment.yml`
 
 The `--deps` option accepts a space-separated list of files or directories.
 Each file will be parsed for declared dependencies; each directory will
@@ -437,8 +438,8 @@ Here is a complete list of configuration directives we support:
   in the repository.
 - `deps_parser_choice`: Manually select which format to use for parsing
   declared dependencies. Must be one of `"requirements.txt"`, `"setup.py"`,
-  `"setup.cfg"`, `"pyproject.toml"`, `"pixi.toml"`, or leave it unset
-  (i.e. the default) for auto-detection (based on filename).
+  `"setup.cfg"`, `"pyproject.toml"`, `"pixi.toml"`, `"environment.yml"`, or
+  leave it unset (i.e. the default) for auto-detection (based on filename).
 - `install-deps`: Automatically install Python dependencies gathered with
   FawltyDeps into a temporary virtual environment. This will use `uv` or `pip`
   to download and install packages from PyPI by default.

fawltydeps/extract_deps.py

@@ -5,6 +5,7 @@
 from pathlib import Path
 from typing import Callable, Iterable, Iterator, NamedTuple, Optional
 
+from fawltydeps.extract_deps_environment_yml import parse_environment_yml
 from fawltydeps.extract_deps_pixi import parse_pixi_toml
 from fawltydeps.extract_deps_pyproject import parse_pyproject_toml
 from fawltydeps.extract_deps_requirements import parse_requirements_txt
@@ -53,6 +54,9 @@ def first_applicable_parser(path: Path) -> Optional[ParserChoice]:
     ParserChoice.PIXI_TOML: ParsingStrategy(
         lambda path: path.name == "pixi.toml", parse_pixi_toml
     ),
+    ParserChoice.ENVIRONMENT_YML: ParsingStrategy(
+        lambda path: path.name == "environment.yml", parse_environment_yml
+    ),
 }
 
 

fawltydeps/types.py

@@ -45,6 +45,7 @@ class ParserChoice(Enum):
     SETUP_CFG = "setup.cfg"
     PYPROJECT_TOML = "pyproject.toml"
     PIXI_TOML = "pixi.toml"
+    ENVIRONMENT_YML = "environment.yml"
 
     def __str__(self) -> str:
         return self.value

tests/conftest.py

@@ -164,7 +164,7 @@ def fake_project(write_tmp_files, fake_venv):  # noqa: C901
             lists of strings (extras/optional deps).
         The dependencies will be written into associated files, formatted
         according to the filenames (must be one of requirements.txt, setup.py,
-        setup.cfg, pyproject.toml, or pixi.toml).
+        setup.cfg, pyproject.toml, pixi.toml, or environment.yml).
     - extra_file_contents: a dict with extra files and their associated contents
         to be forwarded directly to write_tmp_files().
 
@@ -231,6 +231,16 @@ def format_pixi_toml(deps: Deps, extras: ExtraDeps) -> str:
             ret += "\n".join(f'{dep} = "*"' for dep in deps)
         return ret
 
+    def format_environment_yml(deps: Deps, no_extras: ExtraDeps) -> str:
+        assert not no_extras  # not supported
+        return dedent(
+            """\
+                name: MyLib
+
+                dependencies:
+                """
+        ) + "".join(f"  - {dep}\n" for dep in deps)
+
     def format_deps(
         filename: str, all_deps: Union[Deps, Tuple[Deps, ExtraDeps]]
     ) -> str:
@@ -244,6 +254,7 @@ def format_deps(
             "setup.cfg": format_setup_cfg,
             "pyproject.toml": format_pyproject_toml,
             "pixi.toml": format_pixi_toml,
+            "environment.yml": format_environment_yml,
         }
         formatter = formatters.get(Path(filename).name, format_requirements_txt)
         return formatter(deps, extras)

tests/test_cmdline.py

@@ -495,6 +495,7 @@ def test_list_sources__in_varied_project__lists_all_files(fake_project):
             "pyproject.toml": ["foo"],
             "setup.py": ["foo"],
             "setup.cfg": ["foo"],
+            "environment.yml": ["foo"],
         },
         fake_venvs={"my_venv": {}},
     )
@@ -512,6 +513,7 @@ def test_list_sources__in_varied_project__lists_all_files(fake_project):
             "pyproject.toml",
             "setup.py",
             "setup.cfg",
+            "environment.yml",
             str(_site_packages),
         ]
     ]

tests/test_cmdline_options.py

@@ -56,6 +56,7 @@
     "setup.cfg",
     "pyproject.toml",
     "pixi.toml",
+    "environment.yml",
 }
 example_python_stdin = dedent(
     """\

tests/test_deps_parser_determination.py

@@ -30,27 +30,31 @@
             ("setup.cfg", ParserChoice.SETUP_CFG),
             ("pyproject.toml", ParserChoice.PYPROJECT_TOML),
             ("pixi.toml", ParserChoice.PIXI_TOML),
+            ("environment.yml", ParserChoice.ENVIRONMENT_YML),
             ("anything_else", None),
             # in subdir:
             (str(Path("sub", "requirements.txt")), ParserChoice.REQUIREMENTS_TXT),
             (str(Path("sub", "setup.py")), ParserChoice.SETUP_PY),
             (str(Path("sub", "setup.cfg")), ParserChoice.SETUP_CFG),
             (str(Path("sub", "pyproject.toml")), ParserChoice.PYPROJECT_TOML),
             (str(Path("sub", "pixi.toml")), ParserChoice.PIXI_TOML),
+            (str(Path("sub", "environment.yml")), ParserChoice.ENVIRONMENT_YML),
             (str(Path("sub", "anything_else")), None),
             # TODO: Make these absolute paths?
             (str(Path("abs", "requirements.txt")), ParserChoice.REQUIREMENTS_TXT),
             (str(Path("abs", "setup.py")), ParserChoice.SETUP_PY),
             (str(Path("abs", "setup.cfg")), ParserChoice.SETUP_CFG),
             (str(Path("abs", "pyproject.toml")), ParserChoice.PYPROJECT_TOML),
             (str(Path("abs", "pixi.toml")), ParserChoice.PIXI_TOML),
+            (str(Path("abs", "environment.yml")), ParserChoice.ENVIRONMENT_YML),
             (str(Path("abs", "anything_else")), None),
             # using dep file name as a directory name is not supported:
             (str(Path("requirements.txt", "wat")), None),
             (str(Path("setup.py", "wat")), None),
             (str(Path("setup.cfg", "wat")), None),
             (str(Path("pyproject.toml", "wat")), None),
             (str(Path("pixi.toml", "wat")), None),
+            (str(Path("environment.yml", "wat")), None),
             # variations that all map to requirements.txt parser;
             ("requirements-dev.txt", ParserChoice.REQUIREMENTS_TXT),
             ("test-requirements.txt", ParserChoice.REQUIREMENTS_TXT),
@@ -72,6 +76,7 @@ def test_first_applicable_parser(path, expect_choice):
     ParserChoice.SETUP_CFG: "setup.cfg",
     ParserChoice.PYPROJECT_TOML: "pyproject.toml",
     ParserChoice.PIXI_TOML: "pixi.toml",
+    ParserChoice.ENVIRONMENT_YML: "environment.yml",
 }
 PARSER_CHOICE_FILE_NAME_MISMATCH_GRID = {
     pc: [fn for _pc, fn in PARSER_CHOICE_FILE_NAME_MATCH_GRID.items() if pc != _pc]

tests/test_extract_deps_success.py

@@ -721,6 +721,21 @@ def test_find_and_parse_sources__project_with_pixi_toml__returns_list(fake_proje
     assert_unordered_equivalence(actual, expect)
 
 
+def test_find_and_parse_sources__project_with_environment_yml__returns_list(
+    fake_project,
+):
+    tmp_path = fake_project(
+        files_with_declared_deps={
+            "environment.yml": ["numpy", "pandas"],  # dependencies
+        },
+    )
+    expect = ["numpy", "pandas"]
+    settings = Settings(code=set(), deps={tmp_path})
+    deps_sources = list(find_sources(settings, {DepsSource}))
+    actual = collect_dep_names(parse_sources(deps_sources))
+    assert_unordered_equivalence(actual, expect)
+
+
 def test_find_and_parse_sources__project_with_setup_cfg__returns_list(fake_project):
     tmp_path = fake_project(
         files_with_declared_deps={