Setting python-parakeet version and updating install instruciton in r…

…eadme. Version bump

README.md

@@ -90,34 +90,19 @@ conda create -n roodmus_python3_10_4 python=3.10.4
 source activate roodmus_python3_10_4
 
 git clone [email protected]:aj-lab/roodmus.git
-git checkout jgreer/merge_w_analysis
-cd ../
-
-git clone https://github.com/rosalindfranklininstitute/parakeet.git
-cd parakeet
-git checkout 17a0c864f6cfd84b5fd56b60fa446f7b021d338c
-git submodule update --init --recursive
-cd ../
 
 git clone https://gitlab.com/ccpem/ccpem-pipeliner.git
 cd ccpem-pipeliner
 git checkout bedbedbe183ad497dbaa82a638f210d316ba9bae
 cd ../
 
-export CXX=<path>/g++
-export CUDACXX=<path>/bin/nvcc
-export CMAKE_CUDA_ARCHITECTURES=<>
-
 pip install --upgrade pip
 cd roodmus
 pip install e .
 pre-commit install
+pip install pytest
 cd ../
 
-cd parakeet
-pip install -e .
-cd../
-
 cd ccpem-pipeliner
 pip install -e .
 ```

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "roodmus"
-version = "0.0.33"
+version = "0.0.34"
 authors = [
   { name="Joel Greer", email="[email protected]" },
   { name="Maarten Joosten", email="[email protected]" },
@@ -26,6 +26,7 @@ dependencies = [
     "MDAnalysis",
     "umap-learn",
     "scikit-learn>=1.3",
+    "python-parakeet==0.5.1",
 ]
 
 [project.scripts]

src/roodmus/heterogeneity/remove_hydrogens.py

@@ -117,8 +117,10 @@ def read_pdbs(args) -> list[str]:
 
 def main(args):
     # check if gemmi executable is in path
-    assert shutil.which("gemmi"), "Install gemmi cmd line program via"
-    " pip install gemmi-program==0.6.5"
+    assert shutil.which("gemmi"), (
+        "Install gemmi cmd line program via"
+        " pip install gemmi-program==0.6.5"
+    )
 
     # read in the pdb files
     conf_files = get_pdb_list(