fix msgpack dependency issue

extra_requirements.txt

@@ -4,5 +4,4 @@ rdkit>=2020.09.5
 mdtraj
 pdb2pqr>=3.5.2+18
 propka
-openbabel>=3.1.1
-msgpack-python
+openbabel>=3.1.1

package/moleculekit/insert_placeholder_values.py

@@ -12,6 +12,11 @@
 pyproject = toml.load("pyproject.toml")
 deps = pyproject["project"]["dependencies"]
 
+# Fix msgpack pypi package which exists as msgpack-python in conda
+for i in range(len(deps)):
+    if deps[i].startswith("msgpack"):
+        deps[i] = "msgpack-python"
+
 # Fix conda meta.yaml
 with open("package/moleculekit/meta.yaml", "r") as f:
     text = f.read()

pyproject.toml

@@ -9,7 +9,7 @@ classifiers = [
   "Programming Language :: Python :: 3",
   "Operating System :: POSIX :: Linux",
 ]
-dependencies = ["numpy>=1.18.5", "pandas>=1.1.2", "networkx", "tqdm"]
+dependencies = ["numpy>=1.18.5", "pandas>=1.1.2", "networkx", "tqdm", "msgpack"]
 
 [project.urls]
 "Homepage" = "https://github.com/Acellera/moleculekit"