Merge pull request #2834 from nicolossus/update_env_yml

Organize Python dependencies in separate requirements files

.pre-commit-config.yaml

@@ -4,6 +4,7 @@ repos:
     hooks:
       - id: isort
         args: ["--profile", "black", "--thirdparty", "nest"]
+
   - repo: https://github.com/psf/black
     rev: 23.7.0
     hooks:

environment.yml

@@ -1,23 +1,19 @@
-# Conda environment specification for NEST Simulator
+# Conda environment specification for NEST Simulator.
 #
 # This file specifies a conda environment for those who would
 # like to compile NEST or build NEST documentation themselves.
 # If you just want to execute NEST, you should install NEST
 # directly as described in https://www.nest-simulator.org/installation.
 #
-#
 # The environment specification below is comprehensive: it includes
 # all packages required to build and run NEST with OpenMP and MPI
-# parallelisation, GSL-dependent models, NumPy and Pandas-dependent
+# parallelization, GSL-dependent models, NumPy and Pandas-dependent
 # features of PyNEST and examples requiring Matplotlib, and to run
 # the NEST testsuite. It also comprises all tools required to build
-# NEST documentation and to run NEST Server. The requirements for the
-# documentation and server are marked in separate sections below so
-# you can remove them if you would like a leaner environment.
-#
-# NOTE: Do NOT delete the PIP section at the end of the file. Environment files
-#       allow just a single PIP section. All dependencies not satisfied by
-#       conda-forge are placed there.
+# NEST documentation and to run NEST Server. The required Python
+# packages are divided in separate requirements files and marked in
+# separate sections below so you can remove them if you would like a
+# leaner environment.
 #
 # NOTE: libneurosim, MUSIC and SIONLib are not included in this environment.
 #
@@ -31,85 +27,38 @@ channels:
   - conda-forge
 
 dependencies:
-  # Basics ------------------
-  - python >= 3.8
+
+  - python >= 3.10
   - pip
 
-  # Building NEST -----------
   - cmake >= 3.19
-  - cython
   - openmpi
   - boost >= 1.69
   - gsl >= 1.11
   - libtool
   - readline
   - hdf5
+  - cppcheck
+  - doxygen
+  - graphviz
 
-  # Testing NEST ------------
-  - attrs
-  - pytest
-  - pytest-timeout
-  - pytest-xdist
-  - pytest-pylint
-  - pytest-mypy
-  - pytest-cov
-  - numpy
-  - pandas
-  - scipy
+  # mpi4py must be installed by conda in order to automatically find the path
+  # to OpenMPI installed by conda. Note that mpi4py also is included in
+  # requirements_pynest.txt in case someone wants to build an environment
+  # without conda. When this conda environment is built, the pip installation
+  # of mpi4py will be skipped since it is already installed by conda.
   - mpi4py
-  - data-science-types
-  - h5py
-  - terminaltables
-  - pycodestyle
-  - pydocstyle
-  - rstcheck
-  - mypy[version='>=0.8']
-  - cppcheck
 
-  # Working with NEST ------
-  - ipython
-  - matplotlib
-  - jupyter
-  - jupyterlab
+  - pip:
 
-  # Building NEST documentation
-  - PyYAML>=4.2b1
-  - breathe
-  - csvkit
-  - docutils
-  - doxygen
-  - mock
-  - nbsphinx
-  - numpydoc
-  - path.py
-  - pydot
-  - recommonmark
-  - sphinx >= 4.0.2
-  - sphinx_rtd_theme
-  - tqdm
-  - yamllint
+    # To build and work with PyNEST
+    - -r requirements_pynest.txt
 
-  # Running NEST Server ----
-  - flask
-  - flask_cors
-  - gunicorn
-  - requests
-  - restrictedpython
-  - werkzeug
+    # To run NEST testsuite
+    - -r requirements_testing.txt
 
-  # PIP dependencies -- do not delete
-  - pip:
-    # For testsuite
-    - junitparser >= 2
-    - clang-format == 17.0.4
-    # For documentation
-    - example
-    - Image
-    - sphinx_autobuild
-    - sphinx-copybutton
-    - sphinx_design
-    - sphinx_gallery
-    - sphinx-material
-    - sphinx-tabs
-    - sphinx-notfound-page
-    - sphinxcontrib-mermaid
+    # To build NEST documentation
+    - -r requirements_docs.txt
+
+    # To run NEST Server
+    - -r requirements_nest_server.txt

requirements.txt

@@ -0,0 +1,28 @@
+# Required Python packages for NEST Simulator.
+#
+# This file specifies the required Python packages for those who would
+# like to compile NEST or build NEST documentation themselves.
+# If you just want to execute NEST, you should install NEST
+# directly as described in https://www.nest-simulator.org/installation.
+#
+# Note that this file only specifies the required Python packages and 
+# not the entire software stack needed to build and work with NEST Simulator.
+# To create a conda environment with the entire software stack for NEST
+# Simulator, use the the environment yaml file.
+#
+# The requirements from this file can be installed by
+#
+#     pip install -r requirements.txt
+
+
+# To build and work with PyNEST
+-r requirements_pynest.txt
+
+# To run NEST testsuite
+-r requirements_testing.txt
+
+# To build NEST documentation
+-r requirements_docs.txt
+
+# To run NEST Server
+-r requirements_nest_server.txt

requirements_docs.txt

@@ -0,0 +1,35 @@
+# Required Python packages to build NEST documentation.
+#
+# This file specifies the required Python packages to build the NEST
+# documentation. It is meant for those who would like to compile NEST
+# or build NEST documentation themselves. If you just want to execute
+# NEST, you should install NEST directly as described in
+# https://www.nest-simulator.org/installation.
+#
+# The listed requirements are used to build the conda environment defined
+# in the environment yaml file. If you want to build an environment
+# yourself, e.g., independent of conda, the requirements from this file
+# can be installed by
+#
+#     pip install -r requirements_docs.txt
+
+sphinx >= 4.0.2
+sphinx_rtd_theme
+sphinx_autobuild
+sphinx_gallery
+sphinx-tabs
+sphinx_design
+sphinx-material
+sphinx-copybutton
+sphinx-notfound-page
+sphinxcontrib-mermaid
+nbsphinx
+numpydoc
+example
+Image
+breathe
+csvkit
+docutils
+PyYAML >= 4.2b1
+tqdm
+yamllint

requirements_nest_server.txt

@@ -0,0 +1,20 @@
+# Required Python packages to run NEST Server.
+#
+# This file specifies the required Python packages to run NEST Server.
+# It is meant for those who would like to compile NEST or build NEST 
+# documentation themselves. If you just want to execute NEST, you should 
+# install NEST directly as described in 
+# https://www.nest-simulator.org/installation.
+#
+# The listed requirements are used to build the conda environment defined 
+# in the environment yaml file. If you want to build an environment
+# yourself, e.g., independent of conda, the requirements from this file
+# can be installed by
+#
+#     pip install -r requirements_nest_server.txt
+
+Flask
+flask-cors
+gunicorn
+requests
+RestrictedPython

requirements_pynest.txt

@@ -0,0 +1,29 @@
+# Required Python packages to build and work with PyNEST.
+#
+# This file specifies the required Python packages to build and work
+# with PyNEST. It is meant for those who would like to compile NEST
+# or build NEST documentation themselves. If you just want to execute
+# NEST, you should install NEST directly as described in
+# https://www.nest-simulator.org/installation.
+#
+# The listed requirements are used to build the conda environment defined
+# in the environment yaml file. If you want to build an environment
+# yourself, e.g., independent of conda, the requirements from this file
+# can be installed by
+#
+#     pip install -r requirements_pynest.txt
+
+cython
+numpy
+pandas
+scipy
+matplotlib
+mpi4py
+h5py
+black
+pre-commit
+isort
+notebook
+jupyterlab
+csa
+pydot

requirements_testing.txt

@@ -0,0 +1,30 @@
+# Required Python packages to run the NEST testsuite.
+#
+# This file specifies the required Python packages to run the NEST
+# testsuite. It is meant for those who would like to compile NEST
+# or build NEST documentation themselves. If you just want to execute
+# NEST, you should install NEST directly as described in
+# https://www.nest-simulator.org/installation.
+#
+# The listed requirements are used to build the conda environment defined
+# in the environment yaml file. If you want to build an environment
+# yourself, e.g., independent of conda, the requirements from this file
+# can be installed by
+#
+#     pip install -r requirements_testing.txt
+
+pytest
+pytest-timeout
+pytest-xdist
+pytest-pylint
+pytest-mypy
+pytest-cov
+data-science-types
+terminaltables
+pycodestyle
+pydocstyle
+rstcheck
+mypy >= 0.8
+junitparser >= 2
+clang-format == 17.0.4
+attrs