Draft: Attempt to fix python dependencies

It would be nice to relax the version dependencies in the pyproject.toml but fixing them in the requirement.txt files.

The main issue if we fix all the versions in pyproject.toml:

• Practically it is impossible to install nomad-lab package into an existing python environment eg using a jupyter docker image...

  • it doesn't make sense to uninstall and reinstall different version of numpy pandas just because you want to do a query...
  • use --no-dependencies to ignore package dependencies but then it is hard to install the necessary packages manually...

• Obviously it is the easy way to setup an python environment from scratch but for that purpose you can use the requirement.txt files

pyproject.toml

@@ -14,7 +14,7 @@ license = { file = "LICENSE" }
 requires-python = ">=3.9"
 dependencies = [
     'nptyping==1.4.4',
-    'pandas==1.3.5',
+    'pandas>=1.3.5',
     'cachetools==4.2.4',
     'docstring-parser==0.12',
     'Pint==0.17',
@@ -26,7 +26,7 @@ dependencies = [
     'ase==3.19.0',
     'python-keycloak==0.26.1',
     'elasticsearch-dsl==7.4.0',
-    'pydantic==1.10.5',
+    'pydantic>=1.10.8',
     'jmespath==0.10.0',
     'h5grove>=1.0.0',
     'httpx==0.23.3',
@@ -35,7 +35,7 @@ dependencies = [
     'lxml~=4.6',
     'wrapt~=1.12.1',
     'pyyaml==6.0',
-    'python-magic==0.4.24'
+    'python-magic==0.4.24',
 ]
 
 [project.urls]
@@ -48,7 +48,7 @@ parsing = [
     'netCDF4==1.5.4',
     'h5py==3.6.0',
     'hjson==3.0.2',
-    'scipy==1.7.1',
+    'scipy>=1.7.1',
     'panedr==0.2',
     'parmed==3.0.0',
     'mdtraj==1.9.6',
@@ -71,7 +71,7 @@ infrastructure = [
     'asgiref~=3.5',
     'mongoengine>=0.20',
     'pymongo==3.12.1',
-    'itsdangerous==2.0.1',
+    'itsdangerous>=2.0.1',
     'passlib==1.7.4',
     'python-logstash==0.4.6',
     'gitpython==3.1.24',
@@ -92,7 +92,7 @@ infrastructure = [
     'unidecode==1.3.2',
     'python-json-logger==2.0.2',
     'recommonmark==0.7.1',
-    'jinja2==3.0.3',
+    'jinja2>=3.0.3',
     'rdflib==5.0.0',
     'fastapi==0.92.0',
     'uvicorn[standard]',
@@ -102,6 +102,7 @@ infrastructure = [
     'oauthenticator==15.1.0',
     'validators==0.18.2',
     'joblib>=1.1.0',
+    'devtools>=0.8.0',
     'importlib-metadata~=4.13.0' # Needed because of https://github.com/python/importlib_metadata/issues/411
 ]
 dev = [
@@ -116,19 +117,18 @@ dev = [
     'pylint_plugin_utils==0.7',
     'pylint_mongoengine==0.4.0',
     'pycodestyle==2.8.0',
-    'pytest==3.10.0',
-    'pytest-timeout==1.4.2',
-    'pytest-cov==2.7.1',
+    'pytest>=7.1.0',
+    'pytest-timeout>=1.4.2',
+    'pytest-cov>=2.7.1',
     'rope==0.21.0',
     'names==0.3.0',
     'essential_generators==1.0',
     'twine==3.4.2',
     'python-gitlab==2.10.1',
-    'devtools==0.8.0',
-    'mkdocs==1.2.3',
-    'mkdocs-material==8.1.1',
-    'mkdocs-material-extensions==1.0.3',
-    'mkdocs-macros-plugin==0.6.3',
+    'mkdocs>=1.2.4',
+    'mkdocs-material>=8.1.1',
+    'mkdocs-material-extensions>=1.0.3',
+    'mkdocs-macros-plugin>=0.6.3',
     'aiosmtpd'
 ]
 
@@ -159,3 +159,4 @@ disable_error_code = "import, annotation-unchecked"
 
 
 [tool.setuptools_scm]
+