Andrius Merkys
Andrius Merkys
I want to convert a CSV file to SQL `CREATE TABLE` and `INSERT` statements. However, `csvsql` insists on providing `--db` together with `--insert`. This is strange, as `csvsql` produces `CREATE...
There seem to be Python 3.11 compatibility issues: some of the tests fail, most noticeably `tests/test_setlists.py::test_shuffle`: ``` tests/test_setlists.py:183: _ _ _ _ _ _ _ _ _ _ _ _...
Simbody 3.7 fails TestBigMatrix when built on Debian on mips64el and ppc64el architectures: ``` test 12 Start 12: TestBigMatrix 12: Test command: obj-mips64el-linux-gnuabi64/TestBigMatrix 12: Working Directory: obj-mips64el-linux-gnuabi64/SimTKcommon/tests 12: Test timeout...
This PR adds [InChIKey property](https://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey) for structure entries. InChIKey is a chemical structure descriptor alternative to SMILES (proposed in #368). InChIKey is said to avoid the the ambiguity the SMILES...
In issue #426 I proposed adding more chemical properties to OPTIMADE structures. This PR implements [my suggestion](https://github.com/Materials-Consortia/OPTIMADE/issues/426#issuecomment-1434603619) on representation of chemical connectivity between pairs of sites in OPTIMADE: ```json {...
In #368 SMILES property for structures was proposed. PR #392 was proposed to introduce string-valued SMILES property, however, there were opinions that internal semantics of SMILES strings have to be...
The cited fields in OPTIMADE have quite strictly defined values, IMO: https://github.com/Materials-Consortia/optimade-python-tools/blob/5160a2c47f02d070144a62bd391edc2ca63367af/optimade/models/baseinfo.py#L71-L80 * Items of `formats` must match regex `^(json|_.*)$` * Items of `available_endpoints` are as well limited to the...
The following line: https://github.com/jamesrhester/pycifrw/blob/bd9b7ae234217bb5e10ebf204d2eeafd00611fa3/src/CifFile_module.nw#L561 emits a SyntaxWarning on Python 3.11: ``` CifFile/CifFile_module.py:356 CifFile/CifFile_module.py:356: SyntaxWarning: "is not" with a literal. Did you mean "!="? if do_imports is not 'No': ```
12 tests are failing for v0.2.2: ``` 224 passing (138ms) 12 failing 1) add method overflow should return n: AssertionError [ERR_ASSERTION]: 4294967294 == -2 + expected - actual -4294967294 +-2...
TwoPaCo is used by [Pufferfish](https://github.com/COMBINE-lab/pufferfish) which currently embeds a patched code copy of TwoPaCo. Patches seem to transform `main()` function to make it callable in C/C++ code circumventing the command...