From 9cfea1da83401514ec0deb1796202fcb17a91673 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 17 Jan 2024 18:14:49 +0100 Subject: [PATCH 1/4] Cleanup (build & output) --- .pre-commit-config.yaml | 3 ++- setup.cfg | 34 ++++++++++++++++++++------------ src/omero_rdf/__init__.py | 13 ++++++------ src/omero_rdf/idr_annotations.py | 21 ++++++++++++-------- 4 files changed, 43 insertions(+), 28 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5975d93..ddab6f0 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -63,10 +63,11 @@ repos: ] - repo: https://github.com/pre-commit/mirrors-mypy - rev: v0.971 + rev: v1.7.1 hooks: - id: mypy language_version: python3 + args: ["--config-file=setup.cfg"] - repo: https://github.com/adrienverge/yamllint.git rev: v1.26.3 diff --git a/setup.cfg b/setup.cfg index d25e30f..ac359f1 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,19 +1,6 @@ [metadata] description-file = README.rst -[mypy] -check_untyped_defs = true -disallow_any_generics = true -disallow_incomplete_defs = true -disallow_untyped_defs = true -no_implicit_optional = true - -[mypy-setup] -disallow_untyped_defs = false - -[mypy-test_rdf] -disallow_untyped_defs = false - # See the docstring in versioneer.py for instructions. Note that you must # re-run 'versioneer.py setup' after changing this section, and commit the # resulting files. @@ -25,3 +12,24 @@ versionfile_source = src/omero_rdf/_version.py versionfile_build = tag_prefix = v parentdir_prefix = src/omero_rdf/ + +[options] +install_requires = + wikidataintegrator + types-entrypoints + +[mypy] +exclude = src/omero/_version.py +check_untyped_defs = true +disallow_incomplete_defs = true +disallow_untyped_defs = true +no_implicit_optional = true +# FIXME +disallow_any_generics = False +ignore_missing_imports = True + +[mypy-setup] +disallow_untyped_defs = false + +[mypy-test_rdf] +disallow_untyped_defs = false diff --git a/src/omero_rdf/__init__.py b/src/omero_rdf/__init__.py index 07566d5..14511cc 100644 --- a/src/omero_rdf/__init__.py +++ b/src/omero_rdf/__init__.py @@ -31,6 +31,10 @@ from omero_marshal import get_encoder from rdflib import BNode, Literal, URIRef +from . import _version + +__version__ = _version.get_versions()["version"] + HELP = """A plugin for exporting rdf from OMERO omero-rdf creates a stream of RDF triples from the starting object that @@ -154,9 +158,9 @@ def handle(self, data: Data) -> None: if output: s, p, o = output if None in (s, p, o): - print(f""" skipping None value: {s} {p} {o}""") + logging.debug("skipping None value: %s %s %s", s, p, o) else: - print(f"""{s.n3():50}\t{p.n3():60}\t{o.n3()} .""") + print(f"""{s.n3()}\t{p.n3()}\t{o.n3()} .""") def rdf( self, data: Data, _id: Optional[Subj] = None @@ -180,7 +184,7 @@ def rdf( raise Exception(f"missing id: {data}") _id = self.get_identity(_type, str_id) if _id in self.cache: - logging.debug(f"# skipping previously seen {_id}") + logging.debug("# skipping previously seen %s", _id) return else: self.cache.add(_id) @@ -344,6 +348,3 @@ def _lookup( if not obj: self.ctx.die(110, f"No such {_type}: {oid}") return obj - -from . import _version -__version__ = _version.get_versions()['version'] diff --git a/src/omero_rdf/idr_annotations.py b/src/omero_rdf/idr_annotations.py index 7823087..9401b1c 100644 --- a/src/omero_rdf/idr_annotations.py +++ b/src/omero_rdf/idr_annotations.py @@ -18,6 +18,7 @@ # with this program; if not, write to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +import logging from typing import Any, Dict, Generator from rdflib import BNode, Literal, Namespace, URIRef @@ -47,14 +48,14 @@ def __call__( ) -> Generator[Triple, None, bool]: ns = data.get("Namespace") - print(f"# handling {ns}") + logging.debug("# handling %s", ns) _type = data.get("@type") _id = data.get("@id") # Workaround matched with change in the main handler if _type is None or "MapAnnotation" not in _type: - print(f"# skipping non-map: {_type}") + logging.debug("# skipping non-map: %s", _type) return False # End workaround @@ -64,7 +65,11 @@ def __call__( thing = self.handler.get_identity("MapAnnotation", data.get("@id")) if container is not None: - yield (container, WDP.P180, thing) # Container depicts thing described in annotation + yield ( + container, + WDP.P180, + thing, + ) # Container depicts thing described in annotation yield (thing, RDF.type, WD.Q35120) # Q35120 = THING @@ -90,7 +95,7 @@ def __call__( ) self.wikidata[value] = cached else: - print(f"# missing {value} in wikidata") + logging.warning("# missing %s in wikidata", value) yield (thing, WDP.P703, cached) elif name == "Pathology Identifier": @@ -152,7 +157,7 @@ def __call__( ) self.wikidata[value] = cached else: - print(f"missing {value} in wikidata") + logging.warning("missing %s in wikidata", value) yield (thing, WDP.P827, cached) # FIXIE P1080? elif name == "Organism Part Identifier": @@ -193,7 +198,7 @@ def __call__( ) self.wikidata[value] = cached else: - print(f"missing {value} in wikidata") + logging.warning("missing %s in wikidata", value) yield (thing, WDP.P827, cached) elif name == "Sex": @@ -202,7 +207,7 @@ def __call__( elif value == "Male": yield (thing, WDP.P21, WD.Q6581097) else: - print(f"unmapped sex value: {value}") + logging.warning("unmapped sex value: %s", value) elif name == "Age": yield (thing, WDP.P3629, Literal(value)) @@ -217,6 +222,6 @@ def __call__( yield (thing, DC.identifier, URIRef(value)) else: - print(f"# unknown key: {name}") + logging.warning("# unknown key: %s", name) return True From d60e7459a564cfdfc59cb21bfc7fdfd62875ba18 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 17 Jan 2024 18:17:24 +0100 Subject: [PATCH 2/4] Clean _version --- setup.cfg | 1 - src/omero_rdf/_version.py | 163 +++++++++++++++++++++++--------------- 2 files changed, 98 insertions(+), 66 deletions(-) diff --git a/setup.cfg b/setup.cfg index ac359f1..18d4067 100644 --- a/setup.cfg +++ b/setup.cfg @@ -19,7 +19,6 @@ install_requires = types-entrypoints [mypy] -exclude = src/omero/_version.py check_untyped_defs = true disallow_incomplete_defs = true disallow_untyped_defs = true diff --git a/src/omero_rdf/_version.py b/src/omero_rdf/_version.py index 06eaffe..8a725b6 100644 --- a/src/omero_rdf/_version.py +++ b/src/omero_rdf/_version.py @@ -1,4 +1,3 @@ - # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build @@ -12,12 +11,12 @@ """Git implementation of _version.py.""" import errno +import functools import os import re import subprocess import sys from typing import Any, Callable, Dict, List, Optional, Tuple -import functools def get_keywords() -> Dict[str, str]: @@ -68,12 +67,14 @@ class NotThisMethod(Exception): def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator """Create decorator to mark a method as the handler of a VCS.""" + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} HANDLERS[vcs][method] = f return f + return decorate @@ -100,10 +101,14 @@ def run_command( try: dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen([command] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None), **popen_kwargs) + process = subprocess.Popen( + [command] + args, + cwd=cwd, + env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr else None), + **popen_kwargs, + ) break except OSError as e: if e.errno == errno.ENOENT: @@ -114,7 +119,7 @@ def run_command( return None, None else: if verbose: - print("unable to find command, tried %s" % (commands,)) + print(f"unable to find command, tried {commands}") return None, None stdout = process.communicate()[0].strip().decode() if process.returncode != 0: @@ -141,15 +146,21 @@ def versions_from_parentdir( for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} + return { + "version": dirname[len(parentdir_prefix) :], + "full-revisionid": None, + "dirty": False, + "error": None, + "date": None, + } rootdirs.append(root) root = os.path.dirname(root) # up a level if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) + print( + "Tried directories %s but none started with prefix %s" + % (str(rootdirs), parentdir_prefix) + ) raise NotThisMethod("rootdir doesn't start with parentdir_prefix") @@ -162,7 +173,7 @@ def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: # _version.py. keywords: Dict[str, str] = {} try: - with open(versionfile_abs, "r") as fobj: + with open(versionfile_abs) as fobj: for line in fobj: if line.strip().startswith("git_refnames ="): mo = re.search(r'=\s*"(.*)"', line) @@ -212,7 +223,7 @@ def git_versions_from_keywords( # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} + tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -221,7 +232,7 @@ def git_versions_from_keywords( # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r'\d', r)} + tags = {r for r in refs if re.search(r"\d", r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -229,32 +240,36 @@ def git_versions_from_keywords( for ref in sorted(tags): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] + r = ref[len(tag_prefix) :] # Filter out refs that exactly match prefix or that don't start # with a number once the prefix is stripped (mostly a concern # when prefix is '') - if not re.match(r'\d', r): + if not re.match(r"\d", r): continue if verbose: print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} + return { + "version": r, + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": None, + "date": date, + } # no suitable tags, so version is "0+unknown", but full hex is still there if verbose: print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} + return { + "version": "0+unknown", + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": "no suitable tags", + "date": None, + } @register_vcs_handler("git", "pieces_from_vcs") def git_pieces_from_vcs( - tag_prefix: str, - root: str, - verbose: bool, - runner: Callable = run_command + tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command ) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. @@ -273,8 +288,7 @@ def git_pieces_from_vcs( env.pop("GIT_DIR", None) runner = functools.partial(runner, env=env) - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=not verbose) + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -282,10 +296,19 @@ def git_pieces_from_vcs( # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner(GITS, [ - "describe", "--tags", "--dirty", "--always", "--long", - "--match", f"{tag_prefix}[[:digit:]]*" - ], cwd=root) + describe_out, rc = runner( + GITS, + [ + "describe", + "--tags", + "--dirty", + "--always", + "--long", + "--match", + f"{tag_prefix}[[:digit:]]*", + ], + cwd=root, + ) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") @@ -300,8 +323,7 @@ def git_pieces_from_vcs( pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], - cwd=root) + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) # --abbrev-ref was added in git-1.6.3 if rc != 0 or branch_name is None: raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") @@ -341,17 +363,16 @@ def git_pieces_from_vcs( dirty = git_describe.endswith("-dirty") pieces["dirty"] = dirty if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] + git_describe = git_describe[: git_describe.rindex("-dirty")] # now we have TAG-NUM-gHEX or HEX if "-" in git_describe: # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) + mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) + pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out return pieces # tag @@ -360,10 +381,12 @@ def git_pieces_from_vcs( if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) + pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format( + full_tag, + tag_prefix, + ) return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] + pieces["closest-tag"] = full_tag[len(tag_prefix) :] # distance: number of commits since tag pieces["distance"] = int(mo.group(2)) @@ -412,8 +435,7 @@ def render_pep440(pieces: Dict[str, Any]) -> str: rendered += ".dirty" else: # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) + rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" return rendered @@ -442,8 +464,7 @@ def render_pep440_branch(pieces: Dict[str, Any]) -> str: rendered = "0" if pieces["branch"] != "master": rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) + rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) if pieces["dirty"]: rendered += ".dirty" return rendered @@ -604,11 +625,13 @@ def render_git_describe_long(pieces: Dict[str, Any]) -> str: def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} + return { + "version": "unknown", + "full-revisionid": pieces.get("long"), + "dirty": None, + "error": pieces["error"], + "date": None, + } if not style or style == "default": style = "pep440" # the default @@ -632,9 +655,13 @@ def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: else: raise ValueError("unknown style '%s'" % style) - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} + return { + "version": rendered, + "full-revisionid": pieces["long"], + "dirty": pieces["dirty"], + "error": None, + "date": pieces.get("date"), + } def get_versions() -> Dict[str, Any]: @@ -648,8 +675,7 @@ def get_versions() -> Dict[str, Any]: verbose = cfg.verbose try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) + return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) except NotThisMethod: pass @@ -658,13 +684,16 @@ def get_versions() -> Dict[str, Any]: # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for _ in cfg.versionfile_source.split('/'): + for _ in cfg.versionfile_source.split("/"): root = os.path.dirname(root) except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to find root of source tree", + "date": None, + } try: pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) @@ -678,6 +707,10 @@ def get_versions() -> Dict[str, Any]: except NotThisMethod: pass - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to compute version", + "date": None, + } From 0856b05feb9e668b71741e434bf8fa7c8f53aea6 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 17 Jan 2024 18:28:10 +0100 Subject: [PATCH 3/4] Migrate to pyproject and setuptools_scm --- .isort.cfg | 2 +- .pre-commit-config.yaml | 1 - pyproject.toml | 71 ++++ setup.cfg | 34 -- setup.py | 79 ----- src/omero_rdf/__init__.py | 4 - src/omero_rdf/_version.py | 716 -------------------------------------- 7 files changed, 72 insertions(+), 835 deletions(-) create mode 100644 pyproject.toml delete mode 100644 setup.cfg delete mode 100755 setup.py delete mode 100644 src/omero_rdf/_version.py diff --git a/.isort.cfg b/.isort.cfg index aa93fa2..9cad21b 100644 --- a/.isort.cfg +++ b/.isort.cfg @@ -1,2 +1,2 @@ [settings] -known_third_party = entrypoints,omero,omero_marshal,omero_rdf,rdflib,setuptools,versioneer,wikidataintegrator +known_third_party = entrypoints,omero,omero_marshal,omero_rdf,rdflib,wikidataintegrator diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ddab6f0..c831db6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -67,7 +67,6 @@ repos: hooks: - id: mypy language_version: python3 - args: ["--config-file=setup.cfg"] - repo: https://github.com/adrienverge/yamllint.git rev: v1.26.3 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..8d2a9e0 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,71 @@ +[build-system] +requires = [ + "setuptools>=60", + "setuptools-scm>=8.0", +] + +[tools.setuptools.dynamic] +version = {attr = "omero_rdf.__version__"} + +[project] +name = "omero-rdf" +readme = "README.rst" +dynamic = ["version"] +description="A plugin for exporting rdf from OMERO" + +requires-python = ">3.8" + +dependencies = [ + "omero-py>=5.8", + "entrypoints", + "types-entrypoints", + "future", + "rdflib", + "omero-marshal", + "wikidataintegrator", +] + +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Environment :: Plugins", + "Intended Audience :: Developers", + "Intended Audience :: End Users/Desktop", + "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Topic :: Software Development :: Libraries :: Python Modules", +] + +keywords = [ + "OMERO.cli", "plugin", +] + +authors = [ + {name = "The Open Microscopy Team"}, +] + +[project.optional-dependencies] +tests = [ + "pytest", + "restview", + "mox3", +] + +[project.urls] +Repository = "https://github.com/German-BioImaging/omero-rdf" +Changelog = "https://github.com/German-BioImaging/omero-rdf/blob/master/CHANGES.txt" + +[project.entry-points."omero_rdf.annotation_handler"] +idr_annotations = "omero_rdf.idr_annotations:IDRAnnotationHandler" + +[tool.setuptools] +package-dir = {""= "src"} + +[tools.mypy] +check_untyped_defs = true +disallow_incomplete_defs = true +disallow_untyped_defs = true +no_implicit_optional = true +disallow_any_generics = false +ignore_missing_imports = true diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 18d4067..0000000 --- a/setup.cfg +++ /dev/null @@ -1,34 +0,0 @@ -[metadata] -description-file = README.rst - -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -VCS = git -style = pep440 -versionfile_source = src/omero_rdf/_version.py -versionfile_build = -tag_prefix = v -parentdir_prefix = src/omero_rdf/ - -[options] -install_requires = - wikidataintegrator - types-entrypoints - -[mypy] -check_untyped_defs = true -disallow_incomplete_defs = true -disallow_untyped_defs = true -no_implicit_optional = true -# FIXME -disallow_any_generics = False -ignore_missing_imports = True - -[mypy-setup] -disallow_untyped_defs = false - -[mypy-test_rdf] -disallow_untyped_defs = false diff --git a/setup.py b/setup.py deleted file mode 100755 index 767c41d..0000000 --- a/setup.py +++ /dev/null @@ -1,79 +0,0 @@ -#!/usr/bin/env python -# -# Copyright (c) 2022 German BioImaging -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU Affero General Public License as -# published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU Affero General Public License for more details. -# -# You should have received a copy of the GNU Affero General Public License -# along with this program. If not, see . -# -# -import os - -import versioneer -from setuptools import setup - - -def read(fname): - """ - Utility function to read the README file. - :rtype : String - """ - return open(os.path.join(os.path.dirname(__file__), fname)).read() - - -version = version = versioneer.get_version() -url = "https://github.com/german-bioimaging/omero-rdf" - -setup( - version=version, - cmdclass=versioneer.get_cmdclass(), - packages=["omero_rdf", "omero.plugins"], - package_dir={"": "src"}, - name="omero-rdf", - description="A plugin for exporting rdf from OMERO", - long_description=read("README.rst"), - classifiers=[ - "Development Status :: 2 - Pre-Alpha", - "Environment :: Plugins", - "Intended Audience :: Developers", - "Intended Audience :: End Users/Desktop", - "License :: OSI Approved :: GNU General Public License v2 " "or later (GPLv2+)", - "Natural Language :: English", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3", - "Topic :: Software Development :: Libraries :: Python Modules", - ], # Get strings from - # http://pypi.python.org/pypi?%3Aaction=list_classifiers - author="OME Team", - author_email="ome-team@openmicroscopy.org", - license="GPL-2.0+", - url="%s" % url, - zip_safe=False, - download_url=f"{url}/v{version}.tar.gz", - install_requires=[ - "omero-py>=5.8", - "entrypoints", - "future", - "rdflib", - "versioneer", - "omero-marshal", - "wikidataintegrator", - ], - python_requires=">=3", - keywords=["OMERO.CLI", "plugin"], - tests_require=["pytest", "restview", "mox3"], - entry_points={ - "omero_rdf.annotation_handler": [ - "idr_annotations = omero_rdf.idr_annotations:IDRAnnotationHandler" - ] - }, -) diff --git a/src/omero_rdf/__init__.py b/src/omero_rdf/__init__.py index 14511cc..d6ee8f9 100644 --- a/src/omero_rdf/__init__.py +++ b/src/omero_rdf/__init__.py @@ -31,10 +31,6 @@ from omero_marshal import get_encoder from rdflib import BNode, Literal, URIRef -from . import _version - -__version__ = _version.get_versions()["version"] - HELP = """A plugin for exporting rdf from OMERO omero-rdf creates a stream of RDF triples from the starting object that diff --git a/src/omero_rdf/_version.py b/src/omero_rdf/_version.py deleted file mode 100644 index 8a725b6..0000000 --- a/src/omero_rdf/_version.py +++ /dev/null @@ -1,716 +0,0 @@ -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. -# Generated by versioneer-0.29 -# https://github.com/python-versioneer/python-versioneer - -"""Git implementation of _version.py.""" - -import errno -import functools -import os -import re -import subprocess -import sys -from typing import Any, Callable, Dict, List, Optional, Tuple - - -def get_keywords() -> Dict[str, str]: - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - VCS: str - style: str - tag_prefix: str - parentdir_prefix: str - versionfile_source: str - verbose: bool - - -def get_config() -> VersioneerConfig: - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "v" - cfg.parentdir_prefix = "src/omero_rdf/" - cfg.versionfile_source = "src/omero_rdf/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY: Dict[str, str] = {} -HANDLERS: Dict[str, Dict[str, Callable]] = {} - - -def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator - """Create decorator to mark a method as the handler of a VCS.""" - - def decorate(f: Callable) -> Callable: - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command( - commands: List[str], - args: List[str], - cwd: Optional[str] = None, - verbose: bool = False, - hide_stderr: bool = False, - env: Optional[Dict[str, str]] = None, -) -> Tuple[Optional[str], Optional[int]]: - """Call the given command(s).""" - assert isinstance(commands, list) - process = None - - popen_kwargs: Dict[str, Any] = {} - if sys.platform == "win32": - # This hides the console window if pythonw.exe is used - startupinfo = subprocess.STARTUPINFO() - startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW - popen_kwargs["startupinfo"] = startupinfo - - for command in commands: - try: - dispcmd = str([command] + args) - # remember shell=False, so use git.cmd on windows, not just git - process = subprocess.Popen( - [command] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - **popen_kwargs, - ) - break - except OSError as e: - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print(f"unable to find command, tried {commands}") - return None, None - stdout = process.communicate()[0].strip().decode() - if process.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, process.returncode - return stdout, process.returncode - - -def versions_from_parentdir( - parentdir_prefix: str, - root: str, - verbose: bool, -) -> Dict[str, Any]: - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for _ in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords: Dict[str, str] = {} - try: - with open(versionfile_abs) as fobj: - for line in fobj: - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - except OSError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords( - keywords: Dict[str, str], - tag_prefix: str, - verbose: bool, -) -> Dict[str, Any]: - """Get version information from git keywords.""" - if "refnames" not in keywords: - raise NotThisMethod("Short version file found") - date = keywords.get("date") - if date is not None: - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = {r.strip() for r in refnames.strip("()").split(",")} - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = {r for r in refs if re.search(r"\d", r)} - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - # Filter out refs that exactly match prefix or that don't start - # with a number once the prefix is stripped (mostly a concern - # when prefix is '') - if not re.match(r"\d", r): - continue - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs( - tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command -) -> Dict[str, Any]: - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - # GIT_DIR can interfere with correct operation of Versioneer. - # It may be intended to be passed to the Versioneer-versioned project, - # but that should not change where we get our version from. - env = os.environ.copy() - env.pop("GIT_DIR", None) - runner = functools.partial(runner, env=env) - - _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=not verbose) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = runner( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - f"{tag_prefix}[[:digit:]]*", - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces: Dict[str, Any] = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root) - # --abbrev-ref was added in git-1.6.3 - if rc != 0 or branch_name is None: - raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") - branch_name = branch_name.strip() - - if branch_name == "HEAD": - # If we aren't exactly on a branch, pick a branch which represents - # the current commit. If all else fails, we are on a branchless - # commit. - branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) - # --contains was added in git-1.5.4 - if rc != 0 or branches is None: - raise NotThisMethod("'git branch --contains' returned error") - branches = branches.split("\n") - - # Remove the first line if we're running detached - if "(" in branches[0]: - branches.pop(0) - - # Strip off the leading "* " from the list of branches. - branches = [branch[2:] for branch in branches] - if "master" in branches: - branch_name = "master" - elif not branches: - branch_name = None - else: - # Pick the first branch that is returned. Good or bad. - branch_name = branches[0] - - pieces["branch"] = branch_name - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparsable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) - pieces["distance"] = len(out.split()) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - # Use only the last line. Previous lines may contain GPG signature - # information. - date = date.splitlines()[-1] - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces: Dict[str, Any]) -> str: - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces: Dict[str, Any]) -> str: - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_branch(pieces: Dict[str, Any]) -> str: - """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . - - The ".dev0" means not master branch. Note that .dev0 sorts backwards - (a feature branch will appear "older" than the master branch). - - Exceptions: - 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0" - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: - """Split pep440 version string at the post-release segment. - - Returns the release segments before the post-release and the - post-release version number (or -1 if no post-release segment is present). - """ - vc = str.split(ver, ".post") - return vc[0], int(vc[1] or 0) if len(vc) == 2 else None - - -def render_pep440_pre(pieces: Dict[str, Any]) -> str: - """TAG[.postN.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post0.devDISTANCE - """ - if pieces["closest-tag"]: - if pieces["distance"]: - # update the post release segment - tag_version, post_version = pep440_split_post(pieces["closest-tag"]) - rendered = tag_version - if post_version is not None: - rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) - else: - rendered += ".post0.dev%d" % (pieces["distance"]) - else: - # no commits, use the tag as the version - rendered = pieces["closest-tag"] - else: - # exception #1 - rendered = "0.post0.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . - - The ".dev0" means not master branch. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["branch"] != "master": - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_old(pieces: Dict[str, Any]) -> str: - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces: Dict[str, Any]) -> str: - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces: Dict[str, Any]) -> str: - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-branch": - rendered = render_pep440_branch(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-post-branch": - rendered = render_pep440_post_branch(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -def get_versions() -> Dict[str, Any]: - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for _ in cfg.versionfile_source.split("/"): - root = os.path.dirname(root) - except NameError: - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None, - } - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } From abe4e4459018c529a6484c7b1dd964c2350cb62c Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Wed, 17 Jan 2024 18:43:15 +0100 Subject: [PATCH 4/4] Remove last references to setup.py --- .github/workflows/publish_pypi.yml | 4 ++-- .omeroci/README | 2 -- .omeroci/release | 13 ------------- 3 files changed, 2 insertions(+), 17 deletions(-) delete mode 100644 .omeroci/README delete mode 100755 .omeroci/release diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml index e64f694..0838377 100644 --- a/.github/workflows/publish_pypi.yml +++ b/.github/workflows/publish_pypi.yml @@ -11,8 +11,8 @@ jobs: - uses: actions/setup-python@v2 - name: Build a binary wheel and a source tarball run: | - python -mpip install setuptools versioneer wheel - python setup.py sdist bdist_wheel + python -mpip install setuptools build wheel + python -m build - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') uses: pypa/gh-action-pypi-publish@v1.3.0 diff --git a/.omeroci/README b/.omeroci/README deleted file mode 100644 index 6f24a00..0000000 --- a/.omeroci/README +++ /dev/null @@ -1,2 +0,0 @@ -This directory implements scripts to unify -build and release actions across repos. diff --git a/.omeroci/release b/.omeroci/release deleted file mode 100755 index 433da59..0000000 --- a/.omeroci/release +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env make -f -release: -ifndef VERSION - $(error VERSION is undefined) -endif - git describe --exact - python setup.py sdist - echo twine upload dist/omero-rdf-$(VERSION).tar.gz - -clean: - rm -rf build dist omero-rdf.egg-info *.pyc - -.PHONY: release clean