Use pip install --no-deps to avoid overwiting packages from the conda environment

.circleci/config.yml

@@ -41,6 +41,7 @@ commands:
           command: |
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
+            pip check
             pytest -n 4 --junitxml=test-reports/report.xml
             esmvaltool version
             esmvaltool -- --help
@@ -95,7 +96,7 @@ commands:
             conda env create -n esmvaltool -f environment.yml --verbose
             conda activate esmvaltool
             mamba list >> /logs/conda.txt
-            pip install << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
+            pip install --no-deps << parameters.flags >> ".[<<parameters.extra>>]"> /logs/install.txt 2>&1
             if [[ "<<parameters.flags>>" != *'--editable'* ]]
             then
               rm -r esmvaltool
@@ -135,7 +136,7 @@ jobs:
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
             mkdir /logs
-            pip install .[test] > /logs/install.txt 2>&1
+            pip install --no-deps .[test] > /logs/install.txt 2>&1
       - run:
           name: Check Python code style and mistakes
           command: |
@@ -206,9 +207,9 @@ jobs:
             conda env create -n esmvaltool -f environment.yml --verbose
             conda activate esmvaltool
             mamba list >> /logs/conda.txt
-            pip install --editable .[develop]
+            pip install --no-deps --editable .[develop]
             git clone https://github.com/ESMValGroup/ESMValCore $HOME/ESMValCore
-            pip install --editable $HOME/ESMValCore[develop]
+            pip install --no-deps --editable $HOME/ESMValCore[develop]
       - log_versions
       - test_and_report
       - run:
@@ -246,7 +247,8 @@ jobs:
             # Install
             conda env create -n esmvaltool -f environment_python.yml
             conda activate esmvaltool
-            pip install .[doc]
+            pip install --no-deps .[doc]
+            pip check
             # Log versions
             dpkg -l > /logs/versions.txt
             conda env export > /logs/environment.yml

doc/sphinx/source/quickstart/installation.rst

@@ -372,7 +372,7 @@ code (called ``ESMValTool`` if you did not choose a different name):
 
 .. code-block:: bash
 
-    pip install --editable '.[develop]'
+    pip install --no-deps --editable '.[develop]'
 
 Using the ``--editable`` flag will cause the installer to create a symbolic link
 from the installation location to your source code, so any changes you make to
@@ -471,7 +471,7 @@ and then install ESMValCore in development mode
 
 .. code-block:: bash
 
-    pip install --editable '.[develop]'
+    pip install --no-deps --editable '.[develop]'
 
 To check that the installation was successful, run
 
@@ -484,7 +484,7 @@ this should show the directory of the source code that you just downloaded.
 If the command above shows a directory inside your conda environment instead,
 e.g. ``~/miniforge3/envs/esmvaltool/lib/python3.11/site-packages/esmvalcore``,
 you may need to manually remove that directory and run
-``pip install --editable '.[develop]'`` again.
+``pip install --no-deps --editable '.[develop]'`` again.
 
 Finally, also install the :ref:`esmvaltool:pre-commit` hooks by running:
 
@@ -688,7 +688,7 @@ trust the usual PyPI URLs you can declare them with the option
 
 .. code-block:: bash
 
-    pip install --trusted-host=pypi.python.org --trusted-host=pypi.org --trusted-host=files.pythonhosted.org -e .[develop]
+    pip install --trusted-host=pypi.python.org --trusted-host=pypi.org --trusted-host=files.pythonhosted.org --no-deps -e .[develop]
 
 If R packages fail to download, you might be able to solve this by
 setting the environment variable ``http_proxy`` to the correct value, e.g.

environment.yml

@@ -80,7 +80,7 @@ dependencies:
   # Python packages needed for building docs
   - autodocsumm >=0.2.2
   - nbsphinx
-  - sphinx >=6.1.3
+  - sphinx >=6.1.3,<8.2  # Upper pin is a requirement of nbsphinx 0.9.7
   - pydata-sphinx-theme
   # Python packages needed for development
   - codespell ==2.3.0

environment_osx.yml

@@ -80,7 +80,7 @@ dependencies:
   # Python packages needed for building docs
   - autodocsumm >=0.2.2
   - nbsphinx
-  - sphinx >=6.1.3
+  - sphinx >=6.1.3,<8.2  # Upper pin is a requirement of nbsphinx 0.9.7
   - pydata-sphinx-theme
   # Python packages needed for development
   - codespell ==2.3.0