Merge branch 'develop' into main

.gitignore

+# Don't have Emac's backup files
+*~
+
+# ignore test scripts
+biop-test.py
+junk.py
+
+# ignore some files used for testing
+1ake.1.pdb
+3lre.3.A.pdb
+6xne.pdb
+cmp.cif

.spelling

+Biopython
+CIF
+DBs
+FastA
+Jupyter
+MSA
+ModelCIF
+PAE
+PDB
+PPI
+coevolution
+modeled
+modeling
+multimer
+polypeptide
+pre
+repo
+reproducibility
+subdirectory
\ No newline at end of file

pyproject.toml

+[project]
+name = "alphapulldown-modelcif-converter"
+version = "0.0.1"
+requires-python = "==3.8"
+dependencies = [
+    "modelcif==0.8",
+]
+
+[tool.black]
+line-length = 80
+
+[tool.pylint.MAIN]
+load-plugins = "pylint.extensions.bad_builtin"
+
+[tool.pylint.REPORTS]
+reports = "no"
+
+[tool.pylint.FORMAT]
+max-line-length = 81
+
+[tool.pylint.deprecated_builtins]
+# We want to use proper logging, so we can control *ALL* output bei the Abseil
+# logger, hence: deprecate 'print'
+bad-functions = ["map", "filter", "print"]
+
+# Run the spell check every once in a while, having it enabled always, is too
+# annoying.
+#[tool.pylint.spelling]
+#max-spelling-suggestions = 4
+#
+#spelling-dict = "en_GB"
+#
+#spelling-ignore-comment-directives = "fmt: on,fmt: off,noqa:,noqa,nosec,isort:skip,mypy:"
+#
+#spelling-ignore-words = ""
+#
+#spelling-private-dict-file = ".spelling"
+#
+#spelling-store-unknown-words = false
\ No newline at end of file