Optional Dependencies (#967)

* explore optional dependency implementations make all possible dependencies optional tests passing add min env file add additional_url_patterns add oauth2_provider remove warning about user keys Fix pygments lexer warnings in docs build Add install dependency tip box to plot gizmos. black formatting fix lint Removed lingering references to the old developer tools page Add "Starting with Tethys 5.0..." Update tutorial to require installing plotly optional dep notes for Tethys Portal configuration Fixes typo in GRAVATAR_DEFAULT_SECURE setting Replace deprecated Axes setting in docs. Note: settings.py is updated in master docs for social_auth, mf2, and simple_captcha Reviewed manual production configuration docs for optional args REST API and Terms and conditions optional deps JSON Custom setting optional dependency docs MapLayout and pyshp optional dependency. document template tags most optional dependencies documented * all optional dependencies documented * black * tests add micro metayaml update ci * fix tests * Fix issue with TethysJob update-status callback, optimize the JobsTable Gizmo statuses, and allow sorting of the JobsTable. * Apply suggestions from code review * Fix tests Address reviewer comments * Fix Bokeh gizmo with Bokeh V3 * black * fix tests for python 12 * change load_apps to setup_django and display stdout by default update tutorial docs for optional dependencies remove references to UrlMaps in gizmo docs * black --------- Co-authored-by: sdc50 <[email protected]>
tethysplatform · Nov 9, 2023 · f863b48 · f863b48
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diff --git a/.github/workflows/tethys-release.yml b/.github/workflows/tethys-release.yml
@@ -173,3 +173,45 @@ jobs:
           conda activate tethys;
           echo "Publishing to dev channel...";
           anaconda -t "${{ secrets.CONDA_UPLOAD_TOKEN }}" upload -u ${{ secrets.CONDA_UPLOAD_USER }} -l dev $CONDA_BLD_PATH/noarch/tethys-platform*.tar.bz2 --force;
+
+      # BUILD micro-tethys-platform
+
+      # Generate Conda Recipe With Constrained Dependencies
+      - name: Generate Conda Recipe - micro
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          conda activate tethys;
+          tethys gen metayaml -p minor --micro --overwrite;
+      # Show Tethys Meta
+      - name: Show Tethys Meta - micro
+        run: |
+          cd ..
+          cat ./tethys/conda.recipe/meta.yaml
+      # Build Conda
+      - name: Build Conda - micro
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          conda create -y -c conda-forge -n conda-build conda-build anaconda-client 
+          conda activate conda-build
+          conda config --set anaconda_upload no
+          mkdir -p ~/conda-bld
+          conda-build -c tethysplatform -c conda-forge ./tethys/conda.recipe
+      # Upload to Anaconda Cloud
+      - name: Upload to Conda Release Channel - micro
+        if: ${{ steps.version.outputs.prerelease == '' }}
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          conda activate tethys;
+          echo "Publishing to release channel...";
+          anaconda -t "${{ secrets.CONDA_UPLOAD_TOKEN }}" upload -u ${{ secrets.CONDA_UPLOAD_USER }} $CONDA_BLD_PATH/noarch/micro-tethys-platform*.tar.bz2 --force;
+      - name: Upload to Conda Dev Channel - micro
+        if: ${{ steps.version.outputs.prerelease != '' }}
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          conda activate tethys;
+          echo "Publishing to dev channel...";
+          anaconda -t "${{ secrets.CONDA_UPLOAD_TOKEN }}" upload -u ${{ secrets.CONDA_UPLOAD_USER }} -l dev $CONDA_BLD_PATH/noarch/micro-tethys-platform*.tar.bz2 --force;
diff --git a/.github/workflows/tethys.yml b/.github/workflows/tethys.yml
@@ -217,7 +217,7 @@ jobs:
           conda activate conda-build
           conda config --set anaconda_upload no
           mkdir -p ~/conda-bld
-          conda-build -c tethysplatform -c conda-forge ./tethys/conda.recipe
+          conda-build -c conda-forge ./tethys/conda.recipe
       # Upload Conda No Pull Request No Tag
       - name: Upload Conda No Tag
         if: ${{ github.event_name != 'pull_request' }}
@@ -232,3 +232,42 @@ jobs:
         if: ${{ github.event_name == 'pull_request' }}
         run: |
           echo "Uploading is skipped for pull requests."
+
+      # BUILD micro-tethys-platform
+
+      # Generate Conda Recipe Without Constrained Dependencies
+      - name: Generate Conda Recipe - micro
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          conda activate tethys;
+          tethys gen metayaml --micro --overwrite;
+      # Show Tethys Meta
+      - name: Show Tethys Meta - micro
+        run: |
+          cd ..
+          cat ./tethys/conda.recipe/meta.yaml
+      # Build Conda
+      - name: Build Conda - micro
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          conda create -y -c conda-forge -n conda-build conda-build anaconda-client 
+          conda activate conda-build
+          conda config --set anaconda_upload no
+          mkdir -p ~/conda-bld
+          conda-build -c conda-forge ./tethys/conda.recipe
+      # Upload Conda No Pull Request No Tag
+      - name: Upload Conda No Tag - micro
+        if: ${{ github.event_name != 'pull_request' }}
+        run: |
+          cd ..
+          . ~/miniconda/etc/profile.d/conda.sh;
+          ls ~/conda-bld/noarch
+          conda activate conda-build
+          anaconda -t "${{ secrets.CONDA_UPLOAD_TOKEN }}" upload -u ${{ secrets.CONDA_UPLOAD_USER }} -l dev $CONDA_BLD_PATH/noarch/micro-tethys-platform*.tar.bz2 --force;
+      # No Upload if Pull Request
+      - name: No Upload - micro
+        if: ${{ github.event_name == 'pull_request' }}
+        run: |
+          echo "Uploading is skipped for pull requests."
diff --git a/.gitignore b/.gitignore
@@ -34,4 +34,5 @@ build/
 dist/
 tethys_portal/_version.py
 # Required for docs build
-git-lfs-*/*
+git-lfs-*/*
+conda.recipe/meta.yaml
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -19,26 +19,37 @@ Also, be sure that the system you are using meets the minimum :ref:`system_reqs`
 1. Install the ``tethys-platform`` Conda Package
 ------------------------------------------------
 
-a. To install the ``tethys-platform`` into a new conda environment then run the following commands:
+a. To install ``tethys-platform`` into a new conda environment then run the following commands:
 
 .. code-block:: bash
 
-    conda create -n tethys -c tethysplatform -c conda-forge tethys-platform
+    conda create -n tethys -c conda-forge tethys-platform
 
 .. tip::
 
     **Installation Speedup**
 
     If conda is taking too long to solve the Tethys environment, try using the ``libmamba`` solver: :ref:`libmamba_solver`.
 
+    **Install Micro-Tethys**
+
+    The ``micro-tethys-platform`` conda package is a minimal version of ``tethys-platform``. It has the exact same code base, but doesn't include any of the optional dependencies. As a result the environment is much smaller, but none of the optional features will be enabled. Any of the optional features can be enabled simply by installing the dependencies required by those features (see :ref:`optional_features`).
+
+        .. code-block:: bash
+
+            conda create -n tethys -c tethysplatform -c conda-forge micro-tethys-platform
+
     **Install Development Build**
 
-    To install the latest development build of ``tethys-platform`` add the ``tethysplatform/label/dev`` channel to the list of conda channels::
+    To install the latest development build of ``tethys-platform`` add the ``tethysplatform/label/dev`` channel to the list of conda channels:
+
+        .. code-block:: bash
 
-        conda create -n tethys -c tethysplatform/label/dev -c tethysplatform -c conda-forge tethys-platform
+            conda create -n tethys -c tethysplatform/label/dev -c conda-forge tethys-platform
 
     Alternatively, to install from source refer to the :ref:`developer_installation` docs.
 
+
 2. Activate the Tethys Conda Environment
 ----------------------------------------
 
@@ -51,7 +62,9 @@ Anytime you want to work with Tethys Platform, you'll need to activate the ``tet
 3. Create a :file:`portal_config.yml` File
 ------------------------------------------
 
-To add custom configurations such as the database and other local settings you will need to generate a :file:`portal_config.yml` file. To generate a new template :file:`portal_config.yml` run::
+To add custom configurations such as the database and other local settings you will need to generate a :file:`portal_config.yml` file. To generate a new template :file:`portal_config.yml` run:
+
+.. code-block:: bash
 
     tethys gen portal_config
 
@@ -61,20 +74,24 @@ You can customize your settings in the :file:`portal_config.yml` file after you
 4. Configure the Tethys Database
 --------------------------------
 
-Tethys Platform requires a PostgreSQL database server. There are several options for setting up a DB server: local, docker, or dedicated. For development environments you can use Tethys to create a local server::
+There are several options for setting up a DB server: local, docker, or remote. Tethys Platform uses a local SQLite database by default. For development environments you can use Tethys to create a local server:
+
+.. code-block:: bash
 
     tethys db configure
 
 .. note::
 
-    The tethys db command (:ref:`tethys_db_cmd`) will create a local database server in the directory specified by the ``DIR`` setting in the ``DATABASES`` section of the :file:`portal_config.yml` file. If the value of ``DIR`` is a relative path then the database server will be created relative to directory specified by the ``TETHYS_HOME`` environment variable. By default ``TETHYS_HOME`` is at `~/.tethys`.
+    The tethys db command (:ref:`tethys_db_cmd`) will create a local database file in the location specified by the ``NAME`` setting in the ``DATABASES`` section of the :file:`portal_config.yml` file (by default ``tethys_platform.sqlite``). If the value of ``NAME`` is a relative path then the database file will be created relative to directory specified by the ``TETHYS_HOME`` environment variable. By default ``TETHYS_HOME`` is at `~/.tethys`.
 
-    As an alternative to creating a local database server you can also configure a Docker DB server (see :ref:`using_docker`). A local database server is only recommended for development environments. For production environments please refer to :ref:`production_installation`.
+For additional options for configuring a database see :ref:`database_configuration`
 
 5. Start the Development Server
 -------------------------------
 
-Once you have a database successfully configured you can run the Tethys development server::
+Once you have a database successfully configured you can run the Tethys development server:
+
+.. code-block:: bash
 
     tethys manage start
 
@@ -84,7 +101,7 @@ This will start up a locally running web server. You can access the Tethys Porta
 
     You can customize the port that the server is running on by adding the ``-p`` option.
 
-    ::
+    .. code-block:: bash
 
         tethys manage start -p 8001
 
@@ -110,6 +127,7 @@ Related Docs
 
     installation/system_requirements
     tethys_portal/configuration
+    installation/database_configuration
     installation/conda
     installation/application
     installation/showcase_apps

diff --git a/docs/installation/application.rst b/docs/installation/application.rst
@@ -72,6 +72,18 @@ install.yml
 
 This file is generated with your application scaffold. Dependencies that are listed in the ``install.yml`` will be installed with conda and will honor the specified channel priority. If there are any dependencies listed in the ``setup.py`` that are not specified in the ``install.yml`` then these packages will be installed with pip as part of the setup process. This file should be committed with your application code in order to aid installation on a Tethys Portal.
 
+.. important::
+
+    The ``conda`` sections of the ``install.yml`` file require the ``conda`` library and optionally the ``conda-libmamba-solver`` library to be installed. Starting with Tethys 5.0 or if you are using ``micro-tethys-platform``, you will need to install these libraries using conda or pip as follows:
+
+    .. code-block:: bash
+
+        # conda: conda-forge channel strongly recommended
+        conda install -c conda-forge conda conda-libmamba-solver
+
+        # pip
+        pip install conda
+
 .. literalinclude:: resources/example-install.yml
    :language: yaml
 

diff --git a/docs/installation/production/docker/docker_compose.rst b/docs/installation/production/docker/docker_compose.rst
@@ -305,7 +305,7 @@ c. Add the following contents to each ``.env`` file:
 
     **db.env**
 
-    .. code-block:: env
+    .. code-block:: docker
 
         # Password of the db admin account
         POSTGRES_PASSWORD=please_dont_use_default_passwords
@@ -323,7 +323,7 @@ c. Add the following contents to each ``.env`` file:
 
     **thredds.env**
 
-    .. code-block:: env
+    .. code-block:: docker
 
         # Password of the TDM admin user
         TDM_PW=please_dont_use_default_passwords
@@ -355,7 +355,7 @@ c. Add the following contents to each ``.env`` file:
 
     **web.env**
 
-    .. code-block:: env
+    .. code-block:: docker
 
         # Domain name of server should be first in the list if multiple entries added
         ALLOWED_HOSTS="\"[localhost]\""
@@ -471,7 +471,7 @@ a. Create a :file:`.gitignore` file:
 
 b. Add the following contents to the :file:`.gitignore` file to omit the contents of these directories from being tracked:
 
-    .. code-block:: gitignore
+    .. code-block:: text
 
         data/
         keys/

diff --git a/docs/installation/production/manual/configuration/advanced/images/webanalytics.png b/docs/installation/production/manual/configuration/advanced/images/webanalytics.png
diff --git a/docs/installation/production/manual/configuration/advanced/lockout.rst b/docs/installation/production/manual/configuration/advanced/lockout.rst
@@ -6,6 +6,18 @@ Lockout (Optional)
 
 **Last Updated:** May 2020
 
+.. important::
+
+    This feature requires the ``django-axes`` library to be installed. Starting with Tethys 5.0 or if you are using ``micro-tethys-platform``, you will need to install ``django-axes`` using conda or pip as follows:
+
+    .. code-block:: bash
+
+        # conda: conda-forge channel strongly recommended
+        conda install -c conda-forge django-axes
+
+        # pip
+        pip install django-axes
+
 Tethys Portal includes lockout capabilities to prevent brute-force login attempts. This capability is provided by the `Django Axes <https://django-axes.readthedocs.io/en/latest/>`_ add-on for Django. This document describes the different configuration options that are available for lockout capabilities in Tethys Portal.
 
 .. image:: ./images/locked_out.png