Merge pull request #3370 from jessica-mitchell/update-conda-docs

Update instances of conda with mamba in docs

README.md

@@ -12,7 +12,7 @@
 
 [![Ubuntu version](https://img.shields.io/badge/ubuntu-(PPA)-blue?logo=debian)](https://nest-simulator.readthedocs.io/en/latest/installation/)
 [![Fedora package](https://img.shields.io/fedora/v/nest?logo=fedora)](https://src.fedoraproject.org/rpms/nest)
-[![Conda version](https://img.shields.io/conda/vn/conda-forge/nest-simulator.svg?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/nest-simulator)
+[![conda-forge version](https://img.shields.io/conda/vn/conda-forge/nest-simulator.svg?logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/nest-simulator)
 [![Homebrew version](https://img.shields.io/homebrew/v/nest.svg?logo=apple)](https://formulae.brew.sh/formula/nest)
 [![Docker Image Version](https://img.shields.io/docker/v/nest/nest-simulator?color=blue&label=docker&logo=docker&logoColor=white&sort=semver)](https://hub.docker.com/r/nest/nest-simulator)
 [![Virtual applicance](https://img.shields.io/badge/VM-v3.7-blue?logo=CodeSandbox)](https://nest-simulator.readthedocs.io/en/latest/installation/livemedia.html#live-media)
@@ -127,5 +127,3 @@ to find out how to install NEST.
 Please cite NEST if you use it in your work.
 
 - You can find all the information for [citing NEST here](https://nest-simulator.readthedocs.io/en/latest/citing-nest.html)
-
-

doc/htmldoc/connect_nest/nest_server.rst

@@ -59,11 +59,11 @@ For native installations, the requirements can be simply installed via ``pip``::
 
   pip3 install Flask Flask-Cors gunicorn RestrictedPython
 
-or by installing the full NEST development environment in case you prefer using ``conda``::
+or by installing the full NEST development environment in case you prefer using ``mamba``::
 
   cd <nest-source-dir>
-  conda env create -p conda/
-  conda activate conda/
+  mamba env create -p mamba/
+  mamba activate mamba/
 
 As an alternative to a native installation, NEST Server is available from the NEST Docker image. Please check out the
 corresponding :ref:`installation instructions <docker>` for more details.

doc/htmldoc/developer_space/guidelines/mailing_list_guidelines.rst

@@ -30,7 +30,7 @@ please follow the guidelines below:
 
       * the steps you took that lead to the problem.
       * the specific error messages you get.
-      * relevant system and version information (e.g.,  Ubuntu 22.04/ NEST 3.5 installed using the Conda package).
+      * relevant system and version information (e.g.,  Ubuntu 22.04/ NEST 3.8 installed using the conda-forge package).
 
 #. Keep topics separate.
 

doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst

@@ -84,30 +84,38 @@ If you have not done so alrealdy first
 Set up your environment
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Using the Conda package (includes everything to build NEST, including documentation)
-````````````````````````````````````````````````````````````````````````````````````
+Using the conda-forge package (includes everything to build NEST, including documentation)
+```````````````````````````````````````````````````````````````````````````````````````````
 
-For details on Conda, see :ref:`conda_tips`
+For details on installation see :ref:`conda_forge_install`
 
 .. code-block:: bash
 
     cd <nest_source_dir>/
-    conda env create -p conda/
-    conda activate conda/
+    mamba env create -p mamba/
+    mamba activate mamba/
 
 If you later on want to deactivate or delete the build environment:
 
 .. code-block:: bash
 
-   conda deactivate
-   rm -rf conda/
+   mamba deactivate
+   rm -rf mamba/
 
 Using pip (includes packages for documentation only)
 ````````````````````````````````````````````````````
 
 If you want to install only a minimal set of packages for building the
 documentation and avoid using Conda, you can use pip:
 
+Create and activate  a Python virtual environment:
+
+.. code-block:: bash
+
+   python -m venv <myvenv>
+
+   source <myvenv>/bin/activate
+
 .. code-block:: bash
 
     pip3 install -r <nest_source_dir>/doc/requirements.txt

doc/htmldoc/developer_space/workflows/nest_with_ides.rst

@@ -25,7 +25,7 @@ Requirements and limitations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 * Focus on single build configuration
-* Assumes all dependencies (OpenMPI, GSL, etc) installed in a Conda environment
+* Assumes all dependencies (OpenMPI, GSL, etc) installed in a Mamba environment
 * Does not support debugging on macOS (because Eclipse does not support lldb)
 * Does not read the NEST `.clang-format` file, so code formatting may
   be incorrect
@@ -62,25 +62,25 @@ Setting up the project
 #. Right click the project and choose ``Properties`` from the context
    menu
 
-   a. Under ``C/C++ Build/Build Variables``, define ``BUILD_DIR`` and ``CONDA_ENV``,
+   a. Under ``C/C++ Build/Build Variables``, define ``BUILD_DIR`` and ``MAMBA_ENV``,
       both of type ``Path``. The first should contain the full path to the build
-      directory you created above, the second the full path to your conda
-      environment, usually something like ``.../miniconda3/envs/nest-dev``.
+      directory you created above, the second the full path to your mamba
+      environment, usually something like ``.../mamba/envs/nest-dev``.
    #. Under ``C/C++ Build – [Tab] Builder Settings``,
 
       #. uncheck ``Use default build command``
       #. set ``Build Command`` to ``make -k -j4 all install`` (adjust
 	 number of processes to your situation)
       #. set ``Build Directory`` to ``${BUILD_DIR}``
    #. Under ``C/C++ Build > Environment``, prepend
-      ``${CONDA_ENV}/bin`` to ``PATH``
+      ``${MAMBA_ENV}/bin`` to ``PATH``
    #. Under ``C/C++ General > Paths and Symbols – [Tab] Includes``, add the
       following two direcories
 
       * ``${BUILD_DIR}/libnestutil`` (contains ``config.h``)
-      * ``${CONDA_ENV}/include`` (all headers from packages provided in conda environment)
+      * ``${mamba_env}/include`` (all headers from packages provided in Mamba environment)
    #. Under ``PyDev - Interpreter/Grammar``, choose the interpreter from
-      your Conda environment (you may need to add it by following the
+      your Mamba environment (you may need to add it by following the
       ``Click here to configure an interpreter not listed`` link and
       then ``Browse for python/pypy exe`` (this temporarily takes you
       to the global Eclipse preferences in a separate window).
@@ -261,7 +261,7 @@ We need several packages installed, before we can become productive with NEST:
 * gsl
 * cmake
 * libtool
-* ipython, python, cython, ... The best way to install all the python requirements is to use `Anaconda <https://store.continuum.io/cshop/anaconda/>`_.
+* ipython, python, cython, ... The best way to install all the python requirements is to use `Mamba <https://mamba.readthedocs.io/en/latest/index.html/>`_.
 
 We present two ways to install the rest: MacPorts and Homebrew. For both versions you need to have Xcode and Xcode command line tools installed:
 

doc/htmldoc/installation/conda_forge.rst

@@ -1,61 +1,58 @@
 .. _conda_forge_install:
 
-Conda forge install
+conda-forge install
 ===================
 
 .. admonition:: osx-arm64: missing random number generators
 
-   Due to a cross-compiling issue in the conda NEST package, some random number 
-   generators are not available if you are using macOS arm64 architecture. 
+   Due to a cross-compiling issue in the conda-forge NEST package, some random number
+   generators are not available if you are using macOS arm64 architecture.
    The available generators are the Mersenne Twister generators `mt19937` and `mt19937_64`.
 
 .. note::
 
-   If you encounter problems installing the NEST conda package and
-   environment, we recommend using Mamba (https://mamba.readthedocs.io).
+   We recommend using Mamba (https://mamba.readthedocs.io).
    Mamba has the advantage of installing conda packages and
    environments more quickly and can be used as a complete drop-in replacement for conda.
 
-1. To keep your conda setup tidy, we recommend that you install NEST into
-   a separate `conda environment <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_
+1. To keep your mamba setup tidy, we recommend that you install NEST into
+   a separate environment
    together with Python packages that you will use when working with NEST;
    see also our :ref:`conda_tips`.
 
    To install the latest version of NEST in a new environment called ``ENVNAME``, just run
 
    .. code-block:: sh
 
-      conda create --name ENVNAME -c conda-forge nest-simulator
+      mamba create --name ENVNAME -c conda-forge nest-simulator
 
    To install additional packages into the environment, just list them together with ``nest-simulator``.
 
    .. code-block:: sh
 
-      conda create --name ENVNAME -c conda-forge nest-simulator jupyterlab seaborn
+      mamba create --name ENVNAME -c conda-forge nest-simulator jupyterlab seaborn
 
 #. To see all NEST versions available via conda, either run
 
    .. code-block:: sh
 
-      conda search -c conda-forge nest-simulator
+      mamba search -c conda-forge nest-simulator
 
-   or browse the `conda forge file list
-   <https://anaconda.org/conda-forge/nest-simulator/files>`_ (note
-   there are multiple pages). To install, e.g., NEST 2.18.0, run
+    To install a specific version  e.g., NEST 2.18.0, run
 
    .. code-block:: sh
 
-      conda create --name nest_2_18_0 -c conda-forge nest-simulator=2.18.0=*
+      mamba create --name nest_2_18_0 -c conda-forge nest-simulator=2.18.0=*
 
    The syntax for this install follows the pattern: ``nest-simulator=<version>=<build_string>``.
 
 #. Activate your environment:
 
    .. code-block:: sh
 
-      conda activate ENVNAME
+      mamba activate ENVNAME
 
 #. Note the following:
 
-   - We currently provide NEST with thread-based parallelization on conda. This should suffice for most
+   - We currently provide NEST with thread-based parallelization on conda-forge. This should suffice for most
      uses on personal computers.

doc/htmldoc/installation/conda_tips.rst

@@ -1,35 +1,27 @@
 .. _conda_tips:
 
-Tips for installing NEST with conda
+Tips for installing NEST with Mamba
 ===================================
 
-.. note:: 
+.. note::
 
-   If you encounter problems installing the NEST conda package and 
-   environment, we recommend using Mamba (https://mamba.readthedocs.io). 
-   Mamba has the advantage of installing conda packages and 
+   We recommend using Mamba (https://mamba.readthedocs.io).
+   Mamba has the advantage of installing conda packages and
    environments more quickly and can be used as a complete drop-in replacement for conda.
 
 This page provides a series of recommendations for installing pre-built NEST with
 conda or to set up conda environments for building NEST and NEST documentation.
 
-Basic conda setup
+Basic mamba setup
 -----------------
 
-Choice of conda base installation
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-We test NEST in conda environments using Miniconda installations and thus recommend
-that you do the same. The recommendations that we provide here will also likely work with a
-full-sized Anaconda installation, but we can only provide limited support for this.
-
-You can either install
+Apple systems
+~~~~~~~~~~~~~
 
-- Miniconda from `<https://docs.conda.io/en/latest/miniconda.html>`_
-- Miniforge from `<https://github.com/conda-forge/miniforge>`_
 
-For Apple systems with an M1 chip, you must at present use Miniforge and
-select the ``arm64 (Apple Silicon)`` installer to create a conda environment
+For Apple systems with an M1 chip, you must at present use `Miniforge
+<https://github.com/conda-forge/miniforge>`_  and
+select the ``arm64 (Apple Silicon)`` installer to create a mamba environment
 that will support native builds of NEST.
 
 
@@ -38,32 +30,29 @@ Keep your base environment empty
 
 Your base environment should be as empty as possible in order to avoid
 conflicts with other environments. Always install packages only in the new
-environments (don't worry about duplicates, conda will link the packages
+environments (don't worry about duplicates, mamba will link the packages
 if they are used in multiple environments, and not produce disk eating copies).
 
 
-Get familiar with conda environments
+Get familiar with mamba environments
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Conda environments are a powerful tool. See the `Conda documentation on Managing Environments
-<https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_
-for more information.
 
 To see which environments are installed on your system, use
 
 .. code:: sh
 
-   conda info --envs
+   mamba info --envs
 
 
-Installing NEST with Conda
---------------------------
+Installing NEST with conda-forge
+--------------------------------
 
-We provide pre-built versions of NEST on `Conda Forge <https://anaconda.org/conda-forge/nest-simulator/files>`_.
-Follow :ref:`these instructions to install NEST from Conda Forge <conda_forge_install>`.
+We provide pre-built versions of NEST on `conda-forge <https://conda-forge.org/docs/>`_.
+Follow :ref:`these instructions to install NEST from conda-forge <conda_forge_install>`.
 
 
-Creating a Conda environment for running and building NEST
+Creating a mamba environment for running and building NEST
 ----------------------------------------------------------
 
 If you want to compile NEST yourself, you can create an environment containing all necessary
@@ -72,31 +61,26 @@ software for running and building NEST by executing the following command from t
 .. code:: sh
 
    cd <nest-source-dir>
-   conda env create -p conda
+   mamba env create -p mamba
 
-This will create an environment in the folder ``conda/``. If you would like to activate the environment, use
+This will create an environment in the folder ``mamba/``. If you would like to activate the environment, use
 
 .. code:: sh
 
-   conda activate conda/
+   mamba activate mamba/
 
-Note that the trailing slash is required for conda not to confuse the path with a named environment (for example when
+Note that the trailing slash is required for mamba not to confuse the path with a named environment (for example when
 using ``--name``).
 
 
 Get a good overview
 -------------------
 
 Obtain a good overview of which packages are installed where. You can use
-``conda env export -n base`` and ``conda env export -n yournestenv``
+``mamba env export -n base`` and ``mamba env export -n yournestenv``
 (replacing the ``yournestenv`` name with whatever you chose). Make
-sure each environment contains all dependencies. One way to make
-this obvious would be to reduce conda stack to ``0`` (see conda documentation on
-`nested activation <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#nested-activation>`_),
-and/or to a certain degree by not auto-activating the base environment (see conda documentation on
-`conda init <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#conda-init>`_).
-Then packages from base do not 'leak' into your new environments.
+sure each environment contains all dependencies.
 
 .. note::
-   Packages from your system will usually also be available in your conda
+   Packages from your system will usually also be available in your mamba
    environment and may cause similar conflicts.

doc/htmldoc/installation/condaenv_install.rst

@@ -1,24 +1,21 @@
 .. _condaenv:
 
-Install from source in a conda environment
+Install from source in a mamba environment
 ==========================================
 
-.. note:: 
+.. note::
 
-   If you encounter problems installing the NEST conda package and 
-   environment, we recommend using Mamba (https://mamba.readthedocs.io). 
-   Mamba has the advantage of installing conda packages and 
+   We recommend using Mamba (https://mamba.readthedocs.io).
+   Mamba has the advantage of installing conda packages and
    environments more quickly and can be used as a complete drop-in replacement for conda.
 
-* Create a conda environment from the `environment.yml <https://github.com/nest/nest-simulator/blob/master/environment.yml>`_ file.
-  We recommend specifying a dedicated location (``-p <path/to/conda/env>``) for your environment.
-  See the `conda documentation <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#specifying-a-location-for-an-environment>`_
-  on using a custom location rather than the default envs folder.
+* Create a mamba environment from the `environment.yml <https://github.com/nest/nest-simulator/blob/master/environment.yml>`_ file.
+  We recommend specifying a dedicated location (``-p <path/to/mamba/env>``) for your environment.
 
 .. code-block:: sh
 
-    conda env create -f nest-simulator/environment.yml --p <path/to/conda/env>
-    conda activate <path/to/conda/env>
+    mamba env create -f nest-simulator/environment.yml --p <path/to/mamba/env>
+    mamba activate <path/to/mamba/env>
 
 * Create a build directory:
 
@@ -32,7 +29,7 @@ Install from source in a conda environment
 
     cd build_dir
 
-* Configure NEST. Add the cmake option ``-CDMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX`` to link nest to your active conda environment.
+* Configure NEST. Add the cmake option ``-CDMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX`` to link nest to your active mamba environment.
   You may need additional ``cmake`` options (see :ref:`cmake_options`).
 
 .. code-block:: sh
@@ -60,5 +57,3 @@ sourcing the script:
 .. note::
 
    To build the developer or user documentation see :ref:`doc_workflow`
-
-