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fix: pycifrw from PyPI is not working with diffpy.structure=3.3.1rc0 #144

Description

@ycexiao

Problem

Running the commands

pip install diffpy.structure==3.3.1rc0
cd /path/to/diffpy.structure
pytest

will get the error

FAILED tests/test_loadstructure.py::TestLoadStructure::test_badfile - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char0(Trying to find one of END, data_heading)
FAILED tests/test_p_cif.py::TestP_cif::test_parse - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char552(Trying to find one of data_value_1, start_sc_line)
FAILED tests/test_p_cif.py::TestP_cif::test_parseFile - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char552(Trying to find one of data_value_1, start_sc_line)
FAILED tests/test_p_cif.py::TestP_cif::test_parseLines - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char565(Trying to find one of data_value_1, start_sc_line)
FAILED tests/test_p_discus.py::TestP_discus::test_spdiameter_parsing - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char0(Trying to find one of END, data_heading)
FAILED tests/test_p_discus.py::TestP_discus::test_stepcut_parsing - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char0(Trying to find one of END, data_heading)
FAILED tests/test_p_pdffit.py::TestP_pdffit::test_spdiameter_parsing - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char0(Trying to find one of END, data_heading)
FAILED tests/test_p_pdffit.py::TestP_pdffit::test_stepcut_parsing - CifFile.yapps3_compiled_rt.YappsSyntaxError: SyntaxError@char0(Trying to find one of END, data_heading)

Reinstall pycifrw from conda-forge can fix this problem.

conda config --add channels conda-forge
conda install pycifrw

Proposed solution

  • Add the instruction to reinstall pycifrw in the installation instructions.
  • Fix the problem so we don't have to reinstall it from conda-forge
  • Remove the reinstalling instruction after it is fixed.

Activity

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