From 0ac145ce1d5947caef47864d082989ec25318ed0 Mon Sep 17 00:00:00 2001 From: Sandro Dias Pinto Vitenti Date: Fri, 23 Oct 2026 10:28:08 -0300 Subject: [PATCH] Declare the packages firecrown and its pip-installed packages use * Behavior change: firecrown installs no longer pull in astropy and fitsio, which nothing in firecrown imports; install them separately if needed * Remove astropy, used only by the example scripts deleted in #689 * Declare clmm and pydantic-core in runtime, since firecrown imports both * Remove the workarounds nothing imports: charset-normalizer, idna, urllib3, cython, fitsio, more-itertools and fuzzywuzzy * Declare the requirements of cobaya and isitgr, installed from PyPI: dill, getdist, packaging, pandas, portalocker, pybobyqa, rapidfuzz, requests, sympy and tqdm * Keep tabulate as a workaround: numcosmo_py's CLI imports it, but conda-forge's numcosmo 0.28.0 does not declare it * Take build from conda-forge as python-build instead of PyPI, and move types-pyyaml to devenv * Re-solve the lockfiles: 70 to 71 packages fewer per environment; pip installs cobaya, isitgr and py-bobyqa, plus mpmath on Python 3.14 --- .github/conda-lock/py3.12.conda-lock.yml | 2970 +++------------------- .github/conda-lock/py3.13.conda-lock.yml | 2969 +++------------------ .github/conda-lock/py3.14.conda-lock.yml | 2969 +++------------------ CONTRIBUTING.md | 2 +- dependencies-validated.yaml | 18 +- dependencies.yaml | 44 +- environment.yml | 31 +- pyproject.toml | 4 +- 8 files changed, 1246 insertions(+), 7761 deletions(-) diff --git a/.github/conda-lock/py3.12.conda-lock.yml b/.github/conda-lock/py3.12.conda-lock.yml index a1700abfe..841898f2f 100644 --- a/.github/conda-lock/py3.12.conda-lock.yml +++ b/.github/conda-lock/py3.12.conda-lock.yml @@ -13,8 +13,8 @@ version: 1 metadata: content_hash: - 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platform: linux-64 - dependencies: {} - url: https://files.pythonhosted.org/packages/bd/24/12818598c362d7f300f18e74db45963dbcb85150324092410c8b49405e42/pyproject_hooks-1.2.0-py3-none-any.whl - hash: - sha256: 9e5c6bfa8dcc30091c74b0cf803c81fdd29d94f01992a7707bc97babb1141913 - category: main - optional: false -- name: pyproject-hooks - version: 1.2.0 - manager: pip - platform: osx-arm64 - dependencies: {} - url: https://files.pythonhosted.org/packages/bd/24/12818598c362d7f300f18e74db45963dbcb85150324092410c8b49405e42/pyproject_hooks-1.2.0-py3-none-any.whl - hash: - sha256: 9e5c6bfa8dcc30091c74b0cf803c81fdd29d94f01992a7707bc97babb1141913 - category: main - optional: false diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 9d0302b88..5c6dd1ff8 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -81,7 +81,7 @@ firecrown ships — the package, its command line tools and the examples. That i broader than what firecrown imports: `compilers` is there for the two-phase `cosmosis-standard-library` installation, `pip` because cobaya is not packaged on conda-forge and has to come from PyPI to complete the environment, and -`astropy`, `camb` and `isitgr` because the examples need them. +`camb` and `isitgr` because the examples need them. `devenv` is what developing, testing and documenting needs — the link checker's `bs4` and `requests` live here, since `make docs-linkcheck` is the only thing diff --git a/dependencies-validated.yaml b/dependencies-validated.yaml index 9de709888..43efa0abe 100644 --- a/dependencies-validated.yaml +++ b/dependencies-validated.yaml @@ -6,37 +6,35 @@ # # The digest records which environment.yml the lockfiles were solved # from as historical metadata; --check verifies constraints from locks. -environment-sha256: "52bad1a39356cd718b23ced5b6cbe6a2174801a7ab5109885c91a87b2c62bd6d" +environment-sha256: "07e547d8fdd98aa996abc2c58f2d45bec50edb462e90d5d8791491e2db4bc6ae" constraints: - astropy: ">=8.0.2,<8.1" camb: ">=1.6.5,<1.7" - charset-normalizer: ">=3.5.1,<3.6" clmm: ">=1.16.10,<1.17" compilers: ">=1.11.0,<1.12" cosmosis: ">=3.25.2,<3.26" cosmosis-build-standard-library: ">=1.3,<1.4" - cython: ">=3.3.0,<3.4" dill: ">=0.4.1,<0.5" - fitsio: ">=1.4.2,<1.5" - fuzzywuzzy: ">=0.18.0,<0.19" getdist: ">=1.7.7,<1.8" - idna: ">=3.20,<3.21" lsstdesc-crow: ">=1.0.12,<1.1" matplotlib-base: ">=3.11.2,<3.12" - more-itertools: ">=11.2.1,<11.3" numcosmo: ">=0.28.0,<0.29" numpy: ">=2.3.5,<2.4" + packaging: ">=26.3,<26.4" + pandas: ">=3.1.0,<3.2" pip: ">=26.2.2,<26.3" portalocker: ">=3.2.0,<3.3" pybobyqa: ">=1.5.0,<1.6" pyccl: ">=3.3.6,<3.4" pydantic: ">=2.14.1,<2.15" + pydantic-core: ">=2.50.1,<2.51" pyyaml: ">=6.0.3,<6.1" + rapidfuzz: ">=3.14.6,<3.15" + requests: ">=2.34.2,<2.35" rich: ">=15.0.0,<15.1" sacc: ">=2.4,<2.5" scipy: ">=1.18.1,<1.19" + sympy: ">=1.14.0,<1.15" tabulate: ">=0.10.0,<0.11" + tqdm: ">=4.70.1,<4.71" typer: ">=0.27.3,<0.28" - types-pyyaml: ">=6.0.12.20260906,<6.1" typing_extensions: ">=4.16.0,<4.17" - urllib3: ">=2.8.0,<2.9" diff --git a/dependencies.yaml b/dependencies.yaml index ec98a4614..4b963dc6c 100644 --- a/dependencies.yaml +++ b/dependencies.yaml @@ -42,18 +42,17 @@ python: ">=3.12" # is imported -- `compilers` is there for the two-phase # cosmosis-standard-library installation, `pip` because cobaya is not packaged # on conda-forge and has to be installed from PyPI to finish the environment, -# and `astropy`, `camb` and `isitgr` are needed to run the examples. What separates this group from `workarounds` is that +# and `camb` and `isitgr` are needed to run the examples. What separates this group from `workarounds` is that # firecrown needs these present, rather than merely needing them bounded. # Generates: firecrown-deps run requirements, pyproject [project.dependencies]. runtime: - - name: astropy - note: examples/cluster_number_counts - name: camb version: "<2.0" - name: compilers pip: false import: false note: two-phase cosmosis-standard-library installation + - name: clmm - name: cobaya conda: false note: cobaya connector; not packaged on conda-forge @@ -85,6 +84,8 @@ runtime: - name: pyccl version: ">=2.8.0" - name: pydantic + - name: pydantic-core + import: pydantic_core - name: pyyaml import: yaml - name: rich @@ -106,8 +107,8 @@ devenv: import: bs4 note: firecrown-link-checker, run by make docs-linkcheck - name: black - - name: build - conda: false + - name: python-build + import: build - name: coverage - name: deno note: quarto rendering @@ -119,8 +120,6 @@ devenv: - name: jupyter - name: linkchecker - name: mypy - - name: pandas - note: tutorials - name: plotnine - name: pygobject-stubs version: "<2.18" @@ -129,8 +128,6 @@ devenv: - name: pytest-cov - name: pytest-json-report - name: pytest-xdist - - name: requests - note: firecrown-link-checker, run by make docs-linkcheck - name: quarto - name: scipy-stubs - name: sphinx @@ -138,6 +135,7 @@ devenv: - name: sphinx-autodoc-typehints - name: sphinx-rtd-theme - name: sphinxcontrib-apidoc + - name: types-pyyaml - name: types-requests - name: griffe @@ -152,19 +150,25 @@ devenv: # than outliving the bug. These have never been part of the pip metadata; give # an entry a `pip` name to change that. workarounds: - - name: charset-normalizer - - name: clmm - note: part of the DESC stack; needed indirectly through lsstdesc-crow - - name: cython - name: dill - - name: fitsio - pip: true - - name: fuzzywuzzy + note: required by cobaya, installed from PyPI - name: getdist - - name: idna - - name: more-itertools + note: required by cobaya, installed from PyPI + - name: packaging + note: required by cobaya and isitgr, installed from PyPI + - name: pandas + note: required by cobaya, installed from PyPI; also the tutorials - name: portalocker + note: required by cobaya, installed from PyPI - name: pybobyqa + note: required by cobaya (as py-bobyqa), installed from PyPI + - name: rapidfuzz + note: required by cobaya, installed from PyPI + - name: requests + note: required by cobaya, installed from PyPI; also firecrown-link-checker + - name: sympy + note: required by isitgr, installed from PyPI - name: tabulate - - name: types-pyyaml - - name: urllib3 + note: imported by numcosmo_py's CLI but not declared by conda-forge's numcosmo 0.28.0; remove once numcosmo declares it + - name: tqdm + note: required by cobaya, installed from PyPI diff --git a/environment.yml b/environment.yml index 3f89c1e38..9c64d2b41 100644 --- a/environment.yml +++ b/environment.yml @@ -3,49 +3,43 @@ channels: - conda-forge dependencies: - alabaster - - astropy # examples/cluster_number_counts - babel - beautifulsoup4 # firecrown-link-checker, run by make docs-linkcheck - black - camb <2.0 - - charset-normalizer - - clmm # part of the DESC stack; needed indirectly through lsstdesc-crow + - clmm - compilers # two-phase cosmosis-standard-library installation - cosmosis >=3.0,<3.26 # 3.26 .mod files need gfortran 15; camb <2.0 holds compilers at 14 - cosmosis-build-standard-library - coverage - - cython - deno # quarto rendering - - dill - - fitsio + - dill # required by cobaya, installed from PyPI - flake8 - flake8-docstrings - - fuzzywuzzy - - getdist + - getdist # required by cobaya, installed from PyPI - glib - graphviz - griffe - hypothesis - - idna - jupyter - linkchecker - lsstdesc-crow - matplotlib-base # firecrown sacc view - - more-itertools - mypy - numcosmo >=0.28,<1.0 - numpy >=2.0,<2.4 - - pandas # tutorials + - packaging # required by cobaya and isitgr, installed from PyPI + - pandas # required by cobaya, installed from PyPI; also the tutorials - pip >=20.1 # installs cobaya, which conda-forge does not package - pip: - - build - cobaya - isitgr - plotnine - - portalocker - - pybobyqa + - portalocker # required by cobaya, installed from PyPI + - pybobyqa # required by cobaya (as py-bobyqa), installed from PyPI - pyccl >=2.8.0 - pydantic + - pydantic-core - pygobject-stubs <2.18 - pylint - pytest @@ -53,9 +47,11 @@ dependencies: - pytest-json-report - pytest-xdist - python >=3.12 + - python-build - pyyaml - quarto - - requests # firecrown-link-checker, run by make docs-linkcheck + - rapidfuzz # required by cobaya, installed from PyPI + - requests # required by cobaya, installed from PyPI; also firecrown-link-checker - rich - sacc >=2.4 - scipy >=1.13 @@ -65,9 +61,10 @@ dependencies: - sphinx-autodoc-typehints - sphinx-rtd-theme - sphinxcontrib-apidoc - - tabulate + - sympy # required by isitgr, installed from PyPI + - tabulate # imported by numcosmo_py's CLI but not declared by conda-forge's numcosmo 0.28.0; remove once numcosmo declares it + - tqdm # required by cobaya, installed from PyPI - typer - types-pyyaml - types-requests - typing_extensions - - urllib3 diff --git a/pyproject.toml b/pyproject.toml index f17fb79b8..4b99311a7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,11 +11,10 @@ description = "DESC Cosmology Likelihood Framework" requires-python = ">=3.12" license-files = ["LICENSE"] dependencies = [ - "astropy", "camb<2.0", + "clmm", "cobaya", "cosmosis>=3.0,<3.26", - "fitsio", "isitgr", "lsstdesc-crow", "matplotlib", @@ -23,6 +22,7 @@ dependencies = [ "numpy>=2.0,<2.4", "pyccl>=2.8.0", "pydantic", + "pydantic-core", "pyyaml", "rich", "sacc>=2.4",