[Bug 1733686] New: Review Request: python-qcelemental - Periodic table, physical constants, and molecule parsing for quantum chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Bug ID: 1733686 Summary: Review Request: python-qcelemental - Periodic table, physical constants, and molecule parsing for quantum chemistry Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: susi.lehtola@iki.fi QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://jussilehtola.fedorapeople.org/python-qcelemental.spec SRPM URL: https://jussilehtola.fedorapeople.org/python-qcelemental-0.5.0-1.fc30.src.rp... Fedora Account System Username: jussilehtola
Description: QCElemental is a resource module for quantum chemistry containing physical constants and periodic table data from NIST and molecule handlers.
Periodic Table and Physical Constants data are pulled from NIST srd144 and srd121, respectively (details) in a renewable manner (class around NIST-published JSON file).
This project also contains a generator, validator, and translator for Molecule QCSchema.
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Susi Lehtola susi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1733680
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1733680 [Bug 1733680] Update psi4 to 1.3 series
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Susi Lehtola susi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Alias| |python-qcelemental
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Susi Lehtola susi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends On| |1733685 (python-pydantic)
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1733685 [Bug 1733685] Review Request: python-pydantic - Data validation using Python type hinting
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Robert-André Mauchin zebob.m@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |zebob.m@gmail.com
--- Comment #1 from Robert-André Mauchin zebob.m@gmail.com --- - Build the docs with Sphinx
- Rename the second README.md file in prep so there is no overwrite
%doc README.md qcelemental/data/README.md
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - Package does not contain duplicates in %files. Note: BUILDSTDERR: warning: File listed twice: /usr/share/doc/python3-qcelemental/README.md See: https://docs.fedoraproject.org/en-US/packaging- guidelines/#_duplicate_files
===== MUST items =====
Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Unknown or generated", "BSD 3-clause "New" or "Revised" License", "*No copyright* BSD (unspecified)", "GNU Lesser General Public License (v3)". 104 files have unknown license. Detailed output of licensecheck in /home/bob/packaging/review/python- qcelemental/review-python-qcelemental/licensecheck.txt [x]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [-]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [x]: Package consistently uses macros (instead of hard-coded directory names). [x]: Package is named according to the Package Naming Guidelines. [x]: Package does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [-]: If the package is a rename of another package, proper Obsoletes and Provides are present. [x]: Requires correct, justified where necessary. [x]: Spec file is legible and written in American English. [-]: Package contains systemd file(s) if in need. [x]: Package is not known to require an ExcludeArch tag. [-]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 10240 bytes in 1 files. [x]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package does not own files or directories owned by other packages. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Permissions on files are set properly. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local
Python: [x]: Python eggs must not download any dependencies during the build process. [x]: A package which is used by another package via an egg interface should provide egg info. [x]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Packages MUST NOT have dependencies (either build-time or runtime) on packages named with the unversioned python- prefix unless no properly versioned package exists. Dependencies on Python packages instead MUST use names beginning with python2- or python3- as appropriate. [x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files [x]: Binary eggs must be removed in %prep
===== SHOULD items =====
Generic: [-]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [x]: Final provides and requires are sane (see attachments). [?]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified.
===== EXTRA items =====
Generic: [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Spec file according to URL is the same as in SRPM.
Rpmlint ------- Checking: python3-qcelemental-0.5.0-1.fc31.noarch.rpm python-qcelemental-0.5.0-1.fc31.src.rpm python3-qcelemental.noarch: W: spelling-error %description -l en_US validator -> lavatorial python3-qcelemental.noarch: E: wrong-script-interpreter /usr/lib/python3.7/site-packages/qcelemental/tests/test_molparse_align_chiral.py testing aligner on enantiomers based on Table 1 of 10.1021/ci100219f aka J Chem Inf Model 2010 50(12) 2129-2140 python3-qcelemental.noarch: E: non-executable-script /usr/lib/python3.7/site-packages/qcelemental/tests/test_molparse_align_chiral.py 644 testing aligner on enantiomers based on Table 1 of 10.1021/ci100219f aka J Chem Inf Model 2010 50(12) 2129-2140 python-qcelemental.src: W: spelling-error %description -l en_US validator -> lavatorial 2 packages and 0 specfiles checked; 2 errors, 2 warnings.
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
--- Comment #2 from Susi Lehtola susi.lehtola@iki.fi --- Thanks for the extremely speedy review, sorry I missed it! Updated spec and srpm at
https://jussilehtola.fedorapeople.org/python-qcelemental.spec https://jussilehtola.fedorapeople.org/python-qcelemental-0.12.0-1.fc31.src.r...
(In reply to Robert-André Mauchin from comment #1)
- Build the docs with Sphinx
Unfortunately they require sphinx-automodapi https://github.com/astropy/sphinx-automodapi which isn't packaged in Fedora. If it becomes available later on, I can enable the docs.
- Rename the second README.md file in prep so there is no overwrite
%doc README.md qcelemental/data/README.md
Actually, the second README.md pertains to the machine generated data files, and is shipped within the package: /usr/lib/python3.7/site-packages/qcelemental/data/README.md so I don't think it needs to be included in the package documentation.
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
--- Comment #3 from Susi Lehtola susi.lehtola@iki.fi --- Dear Robert-André, do these changes suffice? Once this review is complete, I can start to look into updating Psi4.
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Robert-André Mauchin zebob.m@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |POST Assignee|nobody@fedoraproject.org |zebob.m@gmail.com Flags| |fedora-review+
--- Comment #4 from Robert-André Mauchin zebob.m@gmail.com --- LGTM, package approved.
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
--- Comment #5 from Susi Lehtola susi.lehtola@iki.fi --- Thanks for the review!!
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
--- Comment #6 from Gwyn Ciesla gwync@protonmail.com --- (fedscm-admin): The Pagure repository was created at https://src.fedoraproject.org/rpms/python-qcelemental
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Susi Lehtola susi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends On| |1789066
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1789066 [Bug 1789066] Please update python-pint to 0.10.1 on Fedora 31
https://bugzilla.redhat.com/show_bug.cgi?id=1733686 Bug 1733686 depends on bug 1789066, which changed state.
Bug 1789066 Summary: Please update python-pint to 0.10.1 on Fedora 31 https://bugzilla.redhat.com/show_bug.cgi?id=1789066
What |Removed |Added ---------------------------------------------------------------------------- Status|ON_QA |CLOSED Resolution|--- |ERRATA
https://bugzilla.redhat.com/show_bug.cgi?id=1733686 Bug 1733686 depends on bug 1733685, which changed state.
Bug 1733685 Summary: Review Request: python-pydantic - Data validation using Python type hinting https://bugzilla.redhat.com/show_bug.cgi?id=1733685
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |CLOSED Resolution|--- |RAWHIDE
https://bugzilla.redhat.com/show_bug.cgi?id=1733686
Mattia Verga mattia.verga@protonmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |CLOSED Resolution|--- |CURRENTRELEASE Last Closed| |2021-07-17 09:13:26
--- Comment #7 from Mattia Verga mattia.verga@protonmail.com --- Package is in repos
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