2023-02-10T15:17:38,038 Created temporary directory: /tmp/pip-ephem-wheel-cache-43f1e2dz 2023-02-10T15:17:38,043 Created temporary directory: /tmp/pip-build-tracker-tfnyeoeq 2023-02-10T15:17:38,043 Initialized build tracking at /tmp/pip-build-tracker-tfnyeoeq 2023-02-10T15:17:38,044 Created build tracker: /tmp/pip-build-tracker-tfnyeoeq 2023-02-10T15:17:38,044 Entered build tracker: /tmp/pip-build-tracker-tfnyeoeq 2023-02-10T15:17:38,045 Created temporary directory: /tmp/pip-wheel-uosxqrmx 2023-02-10T15:17:38,053 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-02-10T15:17:38,060 Created temporary directory: /tmp/pip-ephem-wheel-cache-v76r8j1q 2023-02-10T15:17:38,116 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-10T15:17:38,123 2 location(s) to search for versions of mgnifyextract: 2023-02-10T15:17:38,123 * https://pypi.org/simple/mgnifyextract/ 2023-02-10T15:17:38,123 * https://www.piwheels.org/simple/mgnifyextract/ 2023-02-10T15:17:38,124 Fetching project page and analyzing links: https://pypi.org/simple/mgnifyextract/ 2023-02-10T15:17:38,125 Getting page https://pypi.org/simple/mgnifyextract/ 2023-02-10T15:17:38,128 Found index url https://pypi.org/simple 2023-02-10T15:17:38,370 Fetched page https://pypi.org/simple/mgnifyextract/ as application/vnd.pypi.simple.v1+json 2023-02-10T15:17:38,372 Skipping link: No binaries permitted for mgnifyextract: https://files.pythonhosted.org/packages/37/be/a4d6e088ec261c42ac7490a0d1b60f29dfe8dc057fc7099657f54d10b581/mgnifyextract-0.0.2-py3-none-any.whl (from https://pypi.org/simple/mgnifyextract/) 2023-02-10T15:17:38,373 Found link https://files.pythonhosted.org/packages/ce/cb/e16a7350f67811dfa3d6b053b8569aba58089b9be36c4b7b01316d6ed575/mgnifyextract-0.0.2.tar.gz (from https://pypi.org/simple/mgnifyextract/), version: 0.0.2 2023-02-10T15:17:38,374 Fetching project page and analyzing links: https://www.piwheels.org/simple/mgnifyextract/ 2023-02-10T15:17:38,374 Getting page https://www.piwheels.org/simple/mgnifyextract/ 2023-02-10T15:17:38,376 Found index url https://www.piwheels.org/simple 2023-02-10T15:17:38,591 Fetched page https://www.piwheels.org/simple/mgnifyextract/ as text/html 2023-02-10T15:17:38,593 Skipping link: not a file: https://www.piwheels.org/simple/mgnifyextract/ 2023-02-10T15:17:38,594 Skipping link: not a file: https://pypi.org/simple/mgnifyextract/ 2023-02-10T15:17:38,627 Given no hashes to check 1 links for project 'mgnifyextract': discarding no candidates 2023-02-10T15:17:38,656 Collecting mgnifyextract==0.0.2 2023-02-10T15:17:38,661 Created temporary directory: /tmp/pip-unpack-_tbpk8mt 2023-02-10T15:17:38,900 Downloading mgnifyextract-0.0.2.tar.gz (7.4 kB) 2023-02-10T15:17:39,007 Added mgnifyextract==0.0.2 from https://files.pythonhosted.org/packages/ce/cb/e16a7350f67811dfa3d6b053b8569aba58089b9be36c4b7b01316d6ed575/mgnifyextract-0.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-tfnyeoeq' 2023-02-10T15:17:39,014 Created temporary directory: /tmp/pip-build-env-_y6e5r0s 2023-02-10T15:17:39,026 Installing build dependencies: started 2023-02-10T15:17:39,028 Running command pip subprocess to install build dependencies 2023-02-10T15:17:41,717 Using pip 23.0 from /home/piwheels/.local/lib/python3.7/site-packages/pip (python 3.7) 2023-02-10T15:17:42,527 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-02-10T15:17:42,581 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-10T15:17:46,493 Collecting setuptools 2023-02-10T15:17:46,747 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.2.0-py3-none-any.whl (1.1 MB) 2023-02-10T15:17:52,570 Installing collected packages: setuptools 2023-02-10T15:17:56,820 Successfully installed setuptools-67.2.0 2023-02-10T15:17:57,266 Installing build dependencies: finished with status 'done' 2023-02-10T15:17:57,279 Getting requirements to build wheel: started 2023-02-10T15:17:57,281 Running command Getting requirements to build wheel 2023-02-10T15:17:58,877 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-02-10T15:17:58,878 warnings.warn(msg, _BetaConfiguration) 2023-02-10T15:17:58,879 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'description' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:17:58,879 !! 2023-02-10T15:17:58,880 ########################################################################## 2023-02-10T15:17:58,880 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:17:58,881 ########################################################################## 2023-02-10T15:17:58,881 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:17:58,882 `description = 'This library extracts Darwin Core datasets from MGnify'` 2023-02-10T15:17:58,882 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:17:58,883 consider this value unless 'description' is listed as `dynamic`. 2023-02-10T15:17:58,883 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:17:58,884 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:17:58,884 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:17:58,885 follow strictly the standard. 2023-02-10T15:17:58,885 To prevent this warning, you can list 'description' under `dynamic` or alternatively 2023-02-10T15:17:58,885 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:17:58,886 configuration. 2023-02-10T15:17:58,887 !! 2023-02-10T15:17:58,887 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:17:58,888 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'readme' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:17:58,888 !! 2023-02-10T15:17:58,889 ########################################################################## 2023-02-10T15:17:58,890 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:17:58,890 ########################################################################## 2023-02-10T15:17:58,891 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:17:58,891 `readme = '# mgnify-extract\n\nThis library extracts Darwin Core datasets from MGnify. API documentation at https://iobis.github.io/mgnify-extract.\n\n## Usage\n\nFind studies:\n\n```python\nfrom mgnifyextract.studies import find_studies\n\nfilters = {\n "lineage": "root:Environmental:Aquatic:Marine",\n "search": "Tara"\n}\nstudies = find_studies(filters, max_results=1)\n```\n\nFetching samples, runs, analyses, and downloads:\n\n```python\nfrom mgnifyextract.studies import get_study\n\nstudy = get_study("MGYS00000462")\n# \n\nsamples = study.get_samples()\n# [, , , ...]\n\nruns = samples[0].get_runs()\n# [, , ]\n\nanalyses = runs[0].get_analyses()\n# [, ]\n\ndownloads = analyses[0].get_downloads()\n# [, , , , , ]\n```\n\nGenerating Darwin Core tables:\n\n```python\nfrom mgnifyextract.studies import get_superstudy_studies\nfrom mgnifyextract.dwc import study_to_dwc\n\nstudy = get_superstudy_studies("atlanteco")[0]\n# \n\nocc, dna = study_to_dwc(study)\n```\n\n## Run scripts\n\n```\nPYTHONPATH=. python scripts/develop.py\n```\n\n## Run module\n\n```\npython -m mgnifyextract\n```\n'` 2023-02-10T15:17:58,892 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:17:58,892 consider this value unless 'readme' is listed as `dynamic`. 2023-02-10T15:17:58,893 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:17:58,894 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:17:58,894 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:17:58,894 follow strictly the standard. 2023-02-10T15:17:58,895 To prevent this warning, you can list 'readme' under `dynamic` or alternatively 2023-02-10T15:17:58,895 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:17:58,895 configuration. 2023-02-10T15:17:58,896 !! 2023-02-10T15:17:58,897 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:17:58,897 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'license' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:17:58,898 !! 2023-02-10T15:17:58,899 ########################################################################## 2023-02-10T15:17:58,899 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:17:58,899 ########################################################################## 2023-02-10T15:17:58,900 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:17:58,901 `license = 'MIT'` 2023-02-10T15:17:58,901 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:17:58,901 consider this value unless 'license' is listed as `dynamic`. 2023-02-10T15:17:58,902 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:17:58,903 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:17:58,903 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:17:58,903 follow strictly the standard. 2023-02-10T15:17:58,904 To prevent this warning, you can list 'license' under `dynamic` or alternatively 2023-02-10T15:17:58,904 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:17:58,905 configuration. 2023-02-10T15:17:58,906 !! 2023-02-10T15:17:58,906 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:17:58,907 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'authors' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:17:58,907 !! 2023-02-10T15:17:58,908 ########################################################################## 2023-02-10T15:17:58,908 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:17:58,908 ########################################################################## 2023-02-10T15:17:58,909 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:17:58,910 `authors = 'Pieter Provoost'` 2023-02-10T15:17:58,910 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:17:58,910 consider this value unless 'authors' is listed as `dynamic`. 2023-02-10T15:17:58,911 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:17:58,912 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:17:58,912 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:17:58,912 follow strictly the standard. 2023-02-10T15:17:58,913 To prevent this warning, you can list 'authors' under `dynamic` or alternatively 2023-02-10T15:17:58,913 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:17:58,913 configuration. 2023-02-10T15:17:58,914 !! 2023-02-10T15:17:58,915 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:17:58,915 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'urls' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:17:58,916 !! 2023-02-10T15:17:58,917 ########################################################################## 2023-02-10T15:17:58,917 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:17:58,917 ########################################################################## 2023-02-10T15:17:58,918 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:17:58,919 `urls = {'Bug Tracker': 'https://github.com/iobis/mgnify-extract/issues', 'repository': 'https://github.com/iobis/mgnify-extract'}` 2023-02-10T15:17:58,919 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:17:58,920 consider this value unless 'urls' is listed as `dynamic`. 2023-02-10T15:17:58,920 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:17:58,921 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:17:58,921 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:17:58,922 follow strictly the standard. 2023-02-10T15:17:58,922 To prevent this warning, you can list 'urls' under `dynamic` or alternatively 2023-02-10T15:17:58,923 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:17:58,923 configuration. 2023-02-10T15:17:58,924 !! 2023-02-10T15:17:58,925 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:17:59,223 running egg_info 2023-02-10T15:17:59,233 writing mgnifyextract.egg-info/PKG-INFO 2023-02-10T15:17:59,237 writing dependency_links to mgnifyextract.egg-info/dependency_links.txt 2023-02-10T15:17:59,242 writing requirements to mgnifyextract.egg-info/requires.txt 2023-02-10T15:17:59,244 writing top-level names to mgnifyextract.egg-info/top_level.txt 2023-02-10T15:17:59,277 reading manifest file 'mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:17:59,287 writing manifest file 'mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:17:59,291 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-02-10T15:17:59,292 warnings.warn(msg) 2023-02-10T15:17:59,457 Getting requirements to build wheel: finished with status 'done' 2023-02-10T15:17:59,481 Installing backend dependencies: started 2023-02-10T15:17:59,483 Running command pip subprocess to install backend dependencies 2023-02-10T15:18:02,168 Using pip 23.0 from /home/piwheels/.local/lib/python3.7/site-packages/pip (python 3.7) 2023-02-10T15:18:02,960 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-02-10T15:18:03,014 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-02-10T15:18:03,859 Collecting wheel 2023-02-10T15:18:03,895 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2023-02-10T15:18:08,768 Installing collected packages: wheel 2023-02-10T15:18:09,051 Creating /tmp/pip-build-env-_y6e5r0s/normal/bin 2023-02-10T15:18:09,056 changing mode of /tmp/pip-build-env-_y6e5r0s/normal/bin/wheel to 755 2023-02-10T15:18:09,082 Successfully installed wheel-0.38.4 2023-02-10T15:18:09,464 Installing backend dependencies: finished with status 'done' 2023-02-10T15:18:09,470 Created temporary directory: /tmp/pip-modern-metadata-8p4xg22j 2023-02-10T15:18:09,476 Preparing metadata (pyproject.toml): started 2023-02-10T15:18:09,478 Running command Preparing metadata (pyproject.toml) 2023-02-10T15:18:10,945 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-02-10T15:18:10,946 warnings.warn(msg, _BetaConfiguration) 2023-02-10T15:18:10,947 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'description' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:10,947 !! 2023-02-10T15:18:10,948 ########################################################################## 2023-02-10T15:18:10,948 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:10,949 ########################################################################## 2023-02-10T15:18:10,949 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:10,950 `description = 'This library extracts Darwin Core datasets from MGnify'` 2023-02-10T15:18:10,950 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:10,951 consider this value unless 'description' is listed as `dynamic`. 2023-02-10T15:18:10,951 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:10,952 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:10,952 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:10,953 follow strictly the standard. 2023-02-10T15:18:10,953 To prevent this warning, you can list 'description' under `dynamic` or alternatively 2023-02-10T15:18:10,954 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:10,954 configuration. 2023-02-10T15:18:10,955 !! 2023-02-10T15:18:10,956 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:10,956 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'readme' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:10,956 !! 2023-02-10T15:18:10,957 ########################################################################## 2023-02-10T15:18:10,957 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:10,958 ########################################################################## 2023-02-10T15:18:10,958 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:10,959 `readme = '# mgnify-extract\n\nThis library extracts Darwin Core datasets from MGnify. API documentation at https://iobis.github.io/mgnify-extract.\n\n## Usage\n\nFind studies:\n\n```python\nfrom mgnifyextract.studies import find_studies\n\nfilters = {\n "lineage": "root:Environmental:Aquatic:Marine",\n "search": "Tara"\n}\nstudies = find_studies(filters, max_results=1)\n```\n\nFetching samples, runs, analyses, and downloads:\n\n```python\nfrom mgnifyextract.studies import get_study\n\nstudy = get_study("MGYS00000462")\n# \n\nsamples = study.get_samples()\n# [, , , ...]\n\nruns = samples[0].get_runs()\n# [, , ]\n\nanalyses = runs[0].get_analyses()\n# [, ]\n\ndownloads = analyses[0].get_downloads()\n# [, , , , , ]\n```\n\nGenerating Darwin Core tables:\n\n```python\nfrom mgnifyextract.studies import get_superstudy_studies\nfrom mgnifyextract.dwc import study_to_dwc\n\nstudy = get_superstudy_studies("atlanteco")[0]\n# \n\nocc, dna = study_to_dwc(study)\n```\n\n## Run scripts\n\n```\nPYTHONPATH=. python scripts/develop.py\n```\n\n## Run module\n\n```\npython -m mgnifyextract\n```\n'` 2023-02-10T15:18:10,960 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:10,960 consider this value unless 'readme' is listed as `dynamic`. 2023-02-10T15:18:10,961 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:10,961 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:10,962 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:10,962 follow strictly the standard. 2023-02-10T15:18:10,963 To prevent this warning, you can list 'readme' under `dynamic` or alternatively 2023-02-10T15:18:10,963 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:10,963 configuration. 2023-02-10T15:18:10,964 !! 2023-02-10T15:18:10,965 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:10,965 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'license' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:10,965 !! 2023-02-10T15:18:10,966 ########################################################################## 2023-02-10T15:18:10,967 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:10,967 ########################################################################## 2023-02-10T15:18:10,967 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:10,968 `license = 'MIT'` 2023-02-10T15:18:10,969 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:10,969 consider this value unless 'license' is listed as `dynamic`. 2023-02-10T15:18:10,970 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:10,970 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:10,971 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:10,971 follow strictly the standard. 2023-02-10T15:18:10,972 To prevent this warning, you can list 'license' under `dynamic` or alternatively 2023-02-10T15:18:10,972 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:10,972 configuration. 2023-02-10T15:18:10,973 !! 2023-02-10T15:18:10,974 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:10,974 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'authors' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:10,974 !! 2023-02-10T15:18:10,975 ########################################################################## 2023-02-10T15:18:10,976 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:10,976 ########################################################################## 2023-02-10T15:18:10,976 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:10,977 `authors = 'Pieter Provoost'` 2023-02-10T15:18:10,978 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:10,978 consider this value unless 'authors' is listed as `dynamic`. 2023-02-10T15:18:10,978 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:10,979 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:10,979 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:10,980 follow strictly the standard. 2023-02-10T15:18:10,980 To prevent this warning, you can list 'authors' under `dynamic` or alternatively 2023-02-10T15:18:10,981 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:10,981 configuration. 2023-02-10T15:18:10,982 !! 2023-02-10T15:18:10,982 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:10,983 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'urls' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:10,983 !! 2023-02-10T15:18:10,984 ########################################################################## 2023-02-10T15:18:10,984 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:10,985 ########################################################################## 2023-02-10T15:18:10,985 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:10,986 `urls = {'Bug Tracker': 'https://github.com/iobis/mgnify-extract/issues', 'repository': 'https://github.com/iobis/mgnify-extract'}` 2023-02-10T15:18:10,987 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:10,987 consider this value unless 'urls' is listed as `dynamic`. 2023-02-10T15:18:10,988 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:10,988 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:10,989 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:10,989 follow strictly the standard. 2023-02-10T15:18:10,989 To prevent this warning, you can list 'urls' under `dynamic` or alternatively 2023-02-10T15:18:10,990 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:10,990 configuration. 2023-02-10T15:18:10,991 !! 2023-02-10T15:18:10,992 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:11,374 running dist_info 2023-02-10T15:18:11,386 creating /tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info 2023-02-10T15:18:11,395 writing /tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/PKG-INFO 2023-02-10T15:18:11,400 writing dependency_links to /tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/dependency_links.txt 2023-02-10T15:18:11,404 writing requirements to /tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/requires.txt 2023-02-10T15:18:11,406 writing top-level names to /tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/top_level.txt 2023-02-10T15:18:11,409 writing manifest file '/tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:18:11,444 reading manifest file '/tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:18:11,454 writing manifest file '/tmp/pip-modern-metadata-8p4xg22j/mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:18:11,456 creating '/tmp/pip-modern-metadata-8p4xg22j/mgnifyextract-0.0.2.dist-info' 2023-02-10T15:18:11,522 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-02-10T15:18:11,522 warnings.warn(msg) 2023-02-10T15:18:11,693 Preparing metadata (pyproject.toml): finished with status 'done' 2023-02-10T15:18:11,708 Source in /tmp/pip-wheel-uosxqrmx/mgnifyextract_a56548322fd7408e8cd3536539ece20e has version 0.0.2, which satisfies requirement mgnifyextract==0.0.2 from https://files.pythonhosted.org/packages/ce/cb/e16a7350f67811dfa3d6b053b8569aba58089b9be36c4b7b01316d6ed575/mgnifyextract-0.0.2.tar.gz 2023-02-10T15:18:11,710 Removed mgnifyextract==0.0.2 from https://files.pythonhosted.org/packages/ce/cb/e16a7350f67811dfa3d6b053b8569aba58089b9be36c4b7b01316d6ed575/mgnifyextract-0.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-tfnyeoeq' 2023-02-10T15:18:11,719 Created temporary directory: /tmp/pip-unpack-ufix9zf_ 2023-02-10T15:18:11,721 Building wheels for collected packages: mgnifyextract 2023-02-10T15:18:11,730 Created temporary directory: /tmp/pip-wheel-joss5ya0 2023-02-10T15:18:11,731 Destination directory: /tmp/pip-wheel-joss5ya0 2023-02-10T15:18:11,736 Building wheel for mgnifyextract (pyproject.toml): started 2023-02-10T15:18:11,738 Running command Building wheel for mgnifyextract (pyproject.toml) 2023-02-10T15:18:13,139 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/pyprojecttoml.py:108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-02-10T15:18:13,141 warnings.warn(msg, _BetaConfiguration) 2023-02-10T15:18:13,141 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'description' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:13,141 !! 2023-02-10T15:18:13,142 ########################################################################## 2023-02-10T15:18:13,143 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:13,143 ########################################################################## 2023-02-10T15:18:13,143 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:13,144 `description = 'This library extracts Darwin Core datasets from MGnify'` 2023-02-10T15:18:13,145 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:13,145 consider this value unless 'description' is listed as `dynamic`. 2023-02-10T15:18:13,146 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:13,146 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:13,147 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:13,147 follow strictly the standard. 2023-02-10T15:18:13,148 To prevent this warning, you can list 'description' under `dynamic` or alternatively 2023-02-10T15:18:13,148 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:13,148 configuration. 2023-02-10T15:18:13,149 !! 2023-02-10T15:18:13,150 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:13,150 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'readme' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:13,151 !! 2023-02-10T15:18:13,152 ########################################################################## 2023-02-10T15:18:13,152 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:13,152 ########################################################################## 2023-02-10T15:18:13,153 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:13,153 `readme = '# mgnify-extract\n\nThis library extracts Darwin Core datasets from MGnify. API documentation at https://iobis.github.io/mgnify-extract.\n\n## Usage\n\nFind studies:\n\n```python\nfrom mgnifyextract.studies import find_studies\n\nfilters = {\n "lineage": "root:Environmental:Aquatic:Marine",\n "search": "Tara"\n}\nstudies = find_studies(filters, max_results=1)\n```\n\nFetching samples, runs, analyses, and downloads:\n\n```python\nfrom mgnifyextract.studies import get_study\n\nstudy = get_study("MGYS00000462")\n# \n\nsamples = study.get_samples()\n# [, , , ...]\n\nruns = samples[0].get_runs()\n# [, , ]\n\nanalyses = runs[0].get_analyses()\n# [, ]\n\ndownloads = analyses[0].get_downloads()\n# [, , , , , ]\n```\n\nGenerating Darwin Core tables:\n\n```python\nfrom mgnifyextract.studies import get_superstudy_studies\nfrom mgnifyextract.dwc import study_to_dwc\n\nstudy = get_superstudy_studies("atlanteco")[0]\n# \n\nocc, dna = study_to_dwc(study)\n```\n\n## Run scripts\n\n```\nPYTHONPATH=. python scripts/develop.py\n```\n\n## Run module\n\n```\npython -m mgnifyextract\n```\n'` 2023-02-10T15:18:13,154 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:13,154 consider this value unless 'readme' is listed as `dynamic`. 2023-02-10T15:18:13,155 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:13,156 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:13,156 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:13,156 follow strictly the standard. 2023-02-10T15:18:13,157 To prevent this warning, you can list 'readme' under `dynamic` or alternatively 2023-02-10T15:18:13,157 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:13,158 configuration. 2023-02-10T15:18:13,159 !! 2023-02-10T15:18:13,159 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:13,159 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'license' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:13,160 !! 2023-02-10T15:18:13,161 ########################################################################## 2023-02-10T15:18:13,161 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:13,161 ########################################################################## 2023-02-10T15:18:13,162 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:13,163 `license = 'MIT'` 2023-02-10T15:18:13,163 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:13,163 consider this value unless 'license' is listed as `dynamic`. 2023-02-10T15:18:13,164 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:13,165 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:13,165 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:13,165 follow strictly the standard. 2023-02-10T15:18:13,166 To prevent this warning, you can list 'license' under `dynamic` or alternatively 2023-02-10T15:18:13,166 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:13,166 configuration. 2023-02-10T15:18:13,167 !! 2023-02-10T15:18:13,168 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:13,168 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'authors' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:13,169 !! 2023-02-10T15:18:13,169 ########################################################################## 2023-02-10T15:18:13,170 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:13,170 ########################################################################## 2023-02-10T15:18:13,171 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:13,171 `authors = 'Pieter Provoost'` 2023-02-10T15:18:13,172 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:13,172 consider this value unless 'authors' is listed as `dynamic`. 2023-02-10T15:18:13,173 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:13,174 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:13,174 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:13,174 follow strictly the standard. 2023-02-10T15:18:13,175 To prevent this warning, you can list 'authors' under `dynamic` or alternatively 2023-02-10T15:18:13,175 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:13,175 configuration. 2023-02-10T15:18:13,176 !! 2023-02-10T15:18:13,177 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:13,177 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:103: _WouldIgnoreField: 'urls' defined outside of `pyproject.toml` would be ignored. 2023-02-10T15:18:13,178 !! 2023-02-10T15:18:13,179 ########################################################################## 2023-02-10T15:18:13,179 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-02-10T15:18:13,179 ########################################################################## 2023-02-10T15:18:13,180 The following seems to be defined outside of `pyproject.toml`: 2023-02-10T15:18:13,181 `urls = {'Bug Tracker': 'https://github.com/iobis/mgnify-extract/issues', 'repository': 'https://github.com/iobis/mgnify-extract'}` 2023-02-10T15:18:13,181 According to the spec (see the link below), however, setuptools CANNOT 2023-02-10T15:18:13,182 consider this value unless 'urls' is listed as `dynamic`. 2023-02-10T15:18:13,182 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-02-10T15:18:13,183 For the time being, `setuptools` will still consider the given value (as a 2023-02-10T15:18:13,183 **transitional** measure), but please note that future releases of setuptools will 2023-02-10T15:18:13,183 follow strictly the standard. 2023-02-10T15:18:13,184 To prevent this warning, you can list 'urls' under `dynamic` or alternatively 2023-02-10T15:18:13,184 remove the `[project]` table from your file and rely entirely on other means of 2023-02-10T15:18:13,185 configuration. 2023-02-10T15:18:13,186 !! 2023-02-10T15:18:13,186 warnings.warn(msg, _WouldIgnoreField) 2023-02-10T15:18:13,529 running bdist_wheel 2023-02-10T15:18:13,560 running build 2023-02-10T15:18:13,561 running build_py 2023-02-10T15:18:13,572 creating build 2023-02-10T15:18:13,573 creating build/lib 2023-02-10T15:18:13,575 creating build/lib/mgnifyextract 2023-02-10T15:18:13,577 copying mgnifyextract/samples.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,581 copying mgnifyextract/util.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,585 copying mgnifyextract/__init__.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,588 copying mgnifyextract/__main__.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,592 copying mgnifyextract/downloads.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,596 copying mgnifyextract/dwc.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,599 copying mgnifyextract/studies.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,603 copying mgnifyextract/analyses.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,607 copying mgnifyextract/runs.py -> build/lib/mgnifyextract 2023-02-10T15:18:13,609 running egg_info 2023-02-10T15:18:13,627 writing mgnifyextract.egg-info/PKG-INFO 2023-02-10T15:18:13,630 writing dependency_links to mgnifyextract.egg-info/dependency_links.txt 2023-02-10T15:18:13,633 writing requirements to mgnifyextract.egg-info/requires.txt 2023-02-10T15:18:13,635 writing top-level names to mgnifyextract.egg-info/top_level.txt 2023-02-10T15:18:13,652 reading manifest file 'mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:18:13,662 writing manifest file 'mgnifyextract.egg-info/SOURCES.txt' 2023-02-10T15:18:13,683 installing to build/bdist.linux-armv7l/wheel 2023-02-10T15:18:13,683 running install 2023-02-10T15:18:13,745 running install_lib 2023-02-10T15:18:13,755 creating build/bdist.linux-armv7l 2023-02-10T15:18:13,756 creating build/bdist.linux-armv7l/wheel 2023-02-10T15:18:13,760 creating build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,762 copying build/lib/mgnifyextract/samples.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,766 copying build/lib/mgnifyextract/util.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,770 copying build/lib/mgnifyextract/__init__.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,774 copying build/lib/mgnifyextract/__main__.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,777 copying build/lib/mgnifyextract/downloads.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,782 copying build/lib/mgnifyextract/dwc.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,785 copying build/lib/mgnifyextract/studies.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,789 copying build/lib/mgnifyextract/analyses.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,793 copying build/lib/mgnifyextract/runs.py -> build/bdist.linux-armv7l/wheel/mgnifyextract 2023-02-10T15:18:13,796 running install_egg_info 2023-02-10T15:18:13,809 Copying mgnifyextract.egg-info to build/bdist.linux-armv7l/wheel/mgnifyextract-0.0.2-py3.7.egg-info 2023-02-10T15:18:13,830 running install_scripts 2023-02-10T15:18:13,860 creating build/bdist.linux-armv7l/wheel/mgnifyextract-0.0.2.dist-info/WHEEL 2023-02-10T15:18:13,865 creating '/tmp/pip-wheel-joss5ya0/.tmp-1re08qfg/mgnifyextract-0.0.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-02-10T15:18:13,871 adding 'mgnifyextract/__init__.py' 2023-02-10T15:18:13,873 adding 'mgnifyextract/__main__.py' 2023-02-10T15:18:13,876 adding 'mgnifyextract/analyses.py' 2023-02-10T15:18:13,879 adding 'mgnifyextract/downloads.py' 2023-02-10T15:18:13,882 adding 'mgnifyextract/dwc.py' 2023-02-10T15:18:13,885 adding 'mgnifyextract/runs.py' 2023-02-10T15:18:13,887 adding 'mgnifyextract/samples.py' 2023-02-10T15:18:13,890 adding 'mgnifyextract/studies.py' 2023-02-10T15:18:13,893 adding 'mgnifyextract/util.py' 2023-02-10T15:18:13,897 adding 'mgnifyextract-0.0.2.dist-info/METADATA' 2023-02-10T15:18:13,899 adding 'mgnifyextract-0.0.2.dist-info/WHEEL' 2023-02-10T15:18:13,901 adding 'mgnifyextract-0.0.2.dist-info/top_level.txt' 2023-02-10T15:18:13,903 adding 'mgnifyextract-0.0.2.dist-info/RECORD' 2023-02-10T15:18:13,906 removing build/bdist.linux-armv7l/wheel 2023-02-10T15:18:13,918 /tmp/pip-build-env-_y6e5r0s/overlay/lib/python3.7/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-02-10T15:18:13,918 warnings.warn(msg) 2023-02-10T15:18:14,090 Building wheel for mgnifyextract (pyproject.toml): finished with status 'done' 2023-02-10T15:18:14,103 Created wheel for mgnifyextract: filename=mgnifyextract-0.0.2-py3-none-any.whl size=8680 sha256=af351513420da78b626ac3fb2326c41fbfa246c42dcb646169a4007f994d6229 2023-02-10T15:18:14,105 Stored in directory: /tmp/pip-ephem-wheel-cache-v76r8j1q/wheels/fa/1e/ab/c6ae56512b7b5dd0ee90611c890b3a120f4c2e339d195c52f2 2023-02-10T15:18:14,130 Successfully built mgnifyextract 2023-02-10T15:18:14,140 Removed build tracker: '/tmp/pip-build-tracker-tfnyeoeq'