From 7cb7a553cd56abef911cda5a5d28abd95f5ed3f8 Mon Sep 17 00:00:00 2001 From: n8sean Date: Wed, 13 Sep 2023 11:21:50 -0700 Subject: [PATCH 1/3] try sphinx updates -- no success --- .github/workflows/python-package.yml | 2 +- docs/conf.py | 1 + poetry.lock | 355 +++++++++--------- pyproject.toml | 33 +- .../illumina/IlluminaBeadArrayFiles.py | 3 +- 5 files changed, 205 insertions(+), 189 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index a519a356..48c3278f 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -62,7 +62,7 @@ jobs: # If conda should be updated before running other commands (Default: 'false') update-conda: true # Python version which should be installed with conda (default: 'Default') - python-version: "3.8" + python-version: 3.8 # Additional channels like 'conda-forge' which can be used to install packages conda-channels: conda-forge, bioconda, default - name: Install 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hash = "sha256:fcc1ebb7561a3e24a6588f7c6ded15d80aec22c66a070c757559b57b17ffd1cb"}, ] [[package]] @@ -3555,4 +3562,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "dfb1b7f6ef9d13971dd6221bf15a88061b30c298b86487b5093fa13608859de9" +content-hash = "670ffd4d211dde90abac419ff73a330316c77dce0630cc0e1e4e9377c22bc7a6" diff --git a/pyproject.toml b/pyproject.toml index 66001813..f604b03b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,16 +25,21 @@ pandas = "^2.0.3" snakemake = "^6.0.0" pysam = "^0.21.0" ryd = "^0.7.1" -pydantic = "^1.10.12" +# pydantic = "^1.10.12" +pydantic = "^1.0.0" +# pydantic = "*" networkx = "^3.1" -Jinja2 = "^3.1.2" +Jinja2 = ">=2.3, <3.0" more-itertools = "^10.1.0" -seaborn = "^0.12.2" -python-ternary = "^1.0.8" +# seaborn = "^0.12.2" +seaborn = "*" +# matplotlib = "^1.0.0" +# python-ternary = "^1.0.8" +python-ternary = "*" tabulate = "^0.8.0" openpyxl = "^3.1.2" -markupsafe = "^2.1.3" -sphinx-prompt = "^1.0.0" +# markupsafe = "^2.1.3" +markupsafe = "<2.1.0" [tool.poetry.dev-dependencies] black = { version = "^19.10b0", allow-prereleases = true } @@ -42,11 +47,8 @@ flake8 = { version = "^5.0.0", python = ">=3.8,<4.0"} snakefmt = "^0.1.4" importlib-metadata = "^3.10.1" pytest = "^7.4.1" -sphinx = "^4.0.0" mypy = "^1.5.1" isort = "^5.12.0" -sphinxcontrib-mermaid = "^0.9.2" -sphinx-rtd-theme = "^1.3.0" pre-commit = "^3.4.0" rstcheck = "^5.0.0" ipykernel = "^6.25.2" @@ -55,11 +57,16 @@ commitizen = "^2.0.0" ptvsd = "^4.3.2" rope = "^1.9.0" pytest-mock = "^3.11.1" -sphinx-pydantic = "^0.1.1" -sphinx-jsonschema = "^1.19.1" Pillow = "^10.0.0" -Sphinx-Substitution-Extensions = "^2022.2.16" -sphinx-click = "^5.0.1" +# sphinx = "<=2.4.0" +sphinx = "*" +sphinxcontrib-mermaid = "*" +sphinx-rtd-theme = "*" +sphinx-prompt = "*" +sphinx-pydantic = "*" +sphinx-jsonschema = "*" +Sphinx-Substitution-Extensions = "*" +sphinx-click = "*" # tomli = "^2.0.1" # req'd for 'codespell' [tool.poetry.scripts] diff --git a/src/cgr_gwas_qc/parsers/illumina/IlluminaBeadArrayFiles.py b/src/cgr_gwas_qc/parsers/illumina/IlluminaBeadArrayFiles.py index e087bfd2..eac78665 100644 --- a/src/cgr_gwas_qc/parsers/illumina/IlluminaBeadArrayFiles.py +++ b/src/cgr_gwas_qc/parsers/illumina/IlluminaBeadArrayFiles.py @@ -329,7 +329,7 @@ def get_base_calls_generic( "The number of reference strand annotations must match the number of loci in the GTC file" ) - for (genotype, snp, strand_annotation) in zip(genotypes, snps, strand_annotations): + for genotype, snp, strand_annotation in zip(genotypes, snps, strand_annotations): ab_genotype = code2genotype[genotype] a_nucleotide = snp[1] b_nucleotide = snp[-2] @@ -572,6 +572,7 @@ def get_normalized_intensities(self, normalization_lookups): Return: The normalized intensities for the sample as a list of (x,y) float tuples """ + normalization_transforms = self.get_normalization_transforms() return [ normalization_transforms[lookup].normalize_intensities(x_raw, y_raw) From a9ccc24207f7ffe571335687d2a5eff1201919ec Mon Sep 17 00:00:00 2001 From: n8sean Date: Wed, 13 Sep 2023 12:38:48 -0700 Subject: [PATCH 2/3] downgrade sphinx related modules for success DOC BUILD --- poetry.lock | 84 ++++++++++++++++++++------------------------------ pyproject.toml | 33 ++++++-------------- 2 files changed, 44 insertions(+), 73 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1bc4d5fc..5cdcad82 100644 --- a/poetry.lock +++ b/poetry.lock @@ -565,13 +565,13 @@ files = [ [[package]] name = "docutils" -version = "0.17.1" +version = "0.18.1" description = "Docutils -- Python Documentation Utilities" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ - {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"}, - {file = "docutils-0.17.1.tar.gz", hash = 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"sphinx-click" -version = "5.0.1" +version = "3.0.1" description = "Sphinx extension that automatically documents click applications" optional = false -python-versions = ">=3.8" +python-versions = ">=3.6" files = [ - {file = "sphinx-click-5.0.1.tar.gz", hash = "sha256:fcc7df15e56e3ff17ebf446cdd316c2eb79580b37c49579fba11e5468802ef25"}, - {file = "sphinx_click-5.0.1-py3-none-any.whl", hash = "sha256:31836ca22f746d3c26cbfdfe0c58edf0bca5783731a0b2e25bb6d59800bb75a1"}, + {file = "sphinx-click-3.0.1.tar.gz", hash = "sha256:9b24c46f3b8f25fc639f47c97ac0361d9f80d48c2ed6b3917de2865bbdbe1785"}, + {file = "sphinx_click-3.0.1-py3-none-any.whl", hash = "sha256:e9ee2237e5a6b6620e9996b8214934afdf8f7f9f9fc082482c77be0e4379038e"}, ] [package.dependencies] @@ -2978,12 +2978,12 @@ sphinx = ">=2.0" [[package]] name = "sphinx-jsonschema" -version = "1.19.1" +version = "1.15" description = "Sphinx extension to display JSON Schema" optional = false python-versions = "*" files = [ - {file = 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"sha256:578afc04eb4f701d9a922f8b75f678d3a1a897fa7a172a9226b92f17553f177a"}, + {file = "Sphinx_Substitution_Extensions-2020.9.30.0-py3-none-any.whl", hash = "sha256:02e543fb64c82a168031d6f64af5d11bdf91d3f06480ffe399c11be87453729f"}, ] [package.dependencies] docutils = ">=0.15" -sphinx = ">=4.0.0" +sphinx = ">=2.0.0" +sphinx-prompt = ">=0.1" [package.extras] -dev = ["autoflake (==1.4)", "black (==22.1.0)", "check-manifest (==0.47)", "doc8 (==0.10.1)", "flake8 (==4.0.1)", "flake8-commas (==2.1.0)", "flake8-quotes (==3.3.1)", "isort (==5.10.1)", "mypy (==0.931)", "pip-check-reqs (==2.3.2)", "pydocstyle (==6.1.1)", "pyenchant (==3.2.2)", "pylint (==2.12.2)", "pyroma (==3.2)", "pytest (==7.0.1)", "pytest-cov (==3.0.0)", "types-docutils (==0.17.5)", "vulture (==2.3)"] -prompt = ["sphinx-prompt (>=0.1)"] +dev = ["autoflake (==1.4)", "black (==20.8b1)", "check-manifest (==0.43)", "doc8 (==0.8.1)", "flake8 (==3.8.3)", "flake8-commas (==2.0.0)", "flake8-quotes (==3.2.0)", "isort (==5.5.4)", "mypy (==0.782)", "pip-check-reqs (==2.1.1)", "pydocstyle (==5.1.1)", "pyenchant (==3.1.1)", "pygithub (==1.53)", "pylint (==2.6.0)", "pyroma (==2.6)", "pytest (==6.1.0)", "pytest-cov (==2.10.1)", "twine (==3.2.0)", "vulture (==2.1)"] [[package]] name = "sphinxcontrib-applehelp" @@ -3104,20 +3102,6 @@ files = [ lint = ["docutils-stubs", "flake8", "mypy"] test = ["html5lib", "pytest"] -[[package]] -name = "sphinxcontrib-jquery" -version = "4.1" -description = "Extension to include jQuery on newer Sphinx releases" -optional = false -python-versions = ">=2.7" -files = [ - {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"}, - {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"}, -] - -[package.dependencies] -Sphinx = ">=1.8" - [[package]] name = "sphinxcontrib-jsmath" version = "1.0.1" @@ -3134,13 +3118,13 @@ test = ["flake8", "mypy", "pytest"] [[package]] name = "sphinxcontrib-mermaid" -version = "0.9.2" +version = "0.4.0" description = "Mermaid diagrams in yours Sphinx powered docs" optional = false -python-versions = ">=3.7" +python-versions = "*" files = [ - {file = "sphinxcontrib-mermaid-0.9.2.tar.gz", hash = "sha256:252ef13dd23164b28f16d8b0205cf184b9d8e2b714a302274d9f59eb708e77af"}, - {file = "sphinxcontrib_mermaid-0.9.2-py3-none-any.whl", hash = "sha256:6795a72037ca55e65663d2a2c1a043d636dc3d30d418e56dd6087d1459d98a5d"}, + {file = "sphinxcontrib-mermaid-0.4.0.tar.gz", hash = "sha256:0ee45ba45b9575505eacdd6212e4e545213f4f93dfa32c7eeca32720dbc3b468"}, + {file = "sphinxcontrib_mermaid-0.4.0-py2.py3-none-any.whl", hash = "sha256:01b3301af659555313e25ebe3cfd6ba209318044b7443148a20d5580f47baa1d"}, ] [[package]] @@ -3562,4 +3546,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "670ffd4d211dde90abac419ff73a330316c77dce0630cc0e1e4e9377c22bc7a6" +content-hash = "8b3b975f0f62657581d3e5e02df48632a3157c1fd47b09ea41cd82ad5cb04a9a" diff --git a/pyproject.toml b/pyproject.toml index f604b03b..c0a84b71 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,21 +25,15 @@ pandas = "^2.0.3" snakemake = "^6.0.0" pysam = "^0.21.0" ryd = "^0.7.1" -# pydantic = "^1.10.12" pydantic = "^1.0.0" -# pydantic = "*" networkx = "^3.1" Jinja2 = ">=2.3, <3.0" more-itertools = "^10.1.0" -# seaborn = "^0.12.2" -seaborn = "*" -# matplotlib = "^1.0.0" -# python-ternary = "^1.0.8" -python-ternary = "*" +seaborn = "^0.12.2" +python-ternary = "^1.0.8" tabulate = "^0.8.0" openpyxl = "^3.1.2" -# markupsafe = "^2.1.3" -markupsafe = "<2.1.0" +markupsafe = "^2.1.3" [tool.poetry.dev-dependencies] black = { version = "^19.10b0", allow-prereleases = true } @@ -58,26 +52,19 @@ ptvsd = "^4.3.2" rope = "^1.9.0" pytest-mock = "^3.11.1" Pillow = "^10.0.0" -# sphinx = "<=2.4.0" -sphinx = "*" -sphinxcontrib-mermaid = "*" -sphinx-rtd-theme = "*" +sphinx = "3.2.1" +sphinxcontrib-mermaid = "0.4.0" +sphinx-rtd-theme = "0.5.0" sphinx-prompt = "*" -sphinx-pydantic = "*" -sphinx-jsonschema = "*" -Sphinx-Substitution-Extensions = "*" -sphinx-click = "*" -# tomli = "^2.0.1" # req'd for 'codespell' +sphinx-pydantic = "0.1.1" +sphinx-jsonschema = "1.15" +Sphinx-Substitution-Extensions = "2020.9.30" +sphinx-click = "3.0.1" [tool.poetry.scripts] cgr = "cgr_gwas_qc.cli:app" legacy_compare = "cgr_gwas_qc.scripts.legacy_compare:app" -# [tool.codespell] -# skip = "*.po,*.ts,poetry.lock" -# # count = -# quiet-level = 3 - [tool.isort] profile = "black" line_length = 100 From d544f5ec5e1e03914a1f6c6575db1fc915bf8c25 Mon Sep 17 00:00:00 2001 From: n8sean Date: Wed, 13 Sep 2023 12:39:39 -0700 Subject: [PATCH 3/3] downgrade sphinx related modules for success DOC BUILD --- docs/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 557717dd..61d7e5df 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -63,7 +63,6 @@ "sphinx-prompt", "sphinx_substitution_extensions", "sphinx_click", - "sphinx-jsonschema", ] todo_include_todos = True