Use pip install --no-deps to avoid overwiting packages from the conda environment (#2829)

Author: bouweandela

.circleci/config.yml

@@ -31,6 +31,7 @@ commands:
             mkdir -p test-reports
             . /opt/conda/etc/profile.d/conda.sh
             conda activate esmvaltool
+            pip check
             pytest -n 4 --junitxml=test-reports/report.xml << parameters.args >>
             esmvaltool version
       - store_test_results:
@@ -54,7 +55,7 @@ commands:
         type: string
         default: "test"
       flags:
-        description: pip install flags
+        description: pip install --no-deps flags
         type: string
         default: ""
       upstream_packages:
@@ -130,7 +131,7 @@ jobs:
             . /opt/conda/etc/profile.d/conda.sh
             mkdir /logs
             conda activate esmvaltool
-            pip install .[test] > /logs/install.txt 2>&1
+            pip install --no-deps .[test] > /logs/install.txt 2>&1
       - test_and_report:
           args: --cov
       - save_cache:
@@ -220,7 +221,8 @@ jobs:
             # Install
             mamba env create -n esmvaltool -f environment.yml
             conda activate esmvaltool
-            pip install .[doc]
+            pip install --no-deps .[doc]
+            pip check
             # Log versions
             dpkg -l | tee /logs/versions.txt
             conda env export | tee /logs/environment.yml

.github/workflows/create-condalock-file.yml

@@ -61,9 +61,10 @@ jobs:
       - name: Show environment contents
         run: conda list
       - name: Install esmvalcore
-        run: pip install -e .[develop]
+        run: pip install --no-deps -e .[develop]
       - name: Run basic commands
         run: |
+          pip check
           esmvaltool --help
           esmvaltool version
       - name: Run pytests

.github/workflows/install-from-condalock-file.yml

@@ -49,7 +49,8 @@ jobs:
       - run: conda create --name esmvaltool-fromlock --file conda-linux-64.lock
       - run: which python
       - run: pip --version
-      - run: pip install -e .[develop]
+      - run: pip install --no-deps -e .[develop]
+      - run: pip check
       - run: esmvaltool --help
       - run: esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - run: pytest -n 2 -m "not installation"

.github/workflows/install-from-pypi.yml

@@ -61,9 +61,10 @@ jobs:
           python -V 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
           pip -V 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/pip_version.txt
       - name: Install
-        run: pip install esmvalcore 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps esmvalcore 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
+          pip check
           esmvaltool --help
           esmvaltool version 2>&1 | tee pip_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
@@ -99,7 +100,7 @@ jobs:
           python -V 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
           pip -V 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/pip_version.txt
       - name: Install
-        run: pip install esmvalcore 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps esmvalcore 2>&1 | tee pip_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
           esmvaltool --help

.github/workflows/install-from-source.yml

@@ -58,9 +58,10 @@ jobs:
           mamba --version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
           python -V 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - name: Install
-        run: pip install -e .[develop] 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps -e .[develop] 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
+          pip check
           esmvaltool --help
           esmvaltool version 2>&1 | tee source_install_linux_artifacts_python_${{ matrix.python-version }}/version.txt
       - name: Upload artifacts
@@ -99,7 +100,7 @@ jobs:
       - name: Force install x64 git
         run: mamba install -c conda-forge git
       - name: Install
-        run: pip install -e .[develop] 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+        run: pip install --no-deps -e .[develop] 2>&1 | tee source_install_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - name: Verify installation
         run: |
           esmvaltool --help

.github/workflows/run-tests-monitor.yml

@@ -40,8 +40,8 @@ jobs:
       - run: mkdir -p test_linux_artifacts_python_${{ matrix.python-version }}
       - run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
       - run: python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
-      - run: pip install pytest-monitor
-      - run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps pytest-monitor
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: pytest -n 2 -m "not installation" --db ../.pymon 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - run: python tests/parse_pymon.py
       - name: Upload artifacts
@@ -76,8 +76,8 @@ jobs:
       - run: conda --version 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/conda_version.txt
       - run: python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: mamba install -c conda-forge git
-      - run: pip install pytest-monitor
-      - run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps pytest-monitor
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
       - run: pytest -n 2 -m "not installation" --db ../.pymon 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/test_report.txt
       - run: python tests/parse_pymon.py

.github/workflows/run-tests.yml

@@ -58,8 +58,9 @@ jobs:
       - run: conda --version 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/conda_version.txt
       - run: python -V 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: conda list
-      - run: pip install -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_linux_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
+      - run: pip check
       - run: |
           pre-commit install
           pre-commit run -a
@@ -97,7 +98,7 @@ jobs:
       - run: python -V 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/python_version.txt
       - run: mamba install -c conda-forge git
       - run: conda list
-      - run: pip install -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
+      - run: pip install --no-deps -e .[develop] 2>&1 | tee test_osx_artifacts_python_${{ matrix.python-version }}/install.txt
       - run: conda list
       - run: |
           pre-commit install

doc/quickstart/install.rst

@@ -63,11 +63,11 @@ Finally, activate the newly created environment
 
     conda activate esmvalcore
 
-and install ESMValCore as well as any remaining dependencies with the command:
+and install ESMValCore with the command:
 
 .. code-block:: bash
 
-    pip install esmvalcore
+    pip install --no-deps esmvalcore
 
 
 Docker installation
@@ -189,10 +189,10 @@ To install from source for development, follow these instructions.
 -  Create the esmvalcore conda environment
    ``conda env create --name esmvalcore --file environment.yml``
 -  Activate the esmvalcore environment: ``conda activate esmvalcore``
--  Install in development mode: ``pip install -e '.[develop]'``. If you
+-  Install in development mode: ``pip install --no-deps -e '.[develop]'``. If you
    are installing behind a proxy that does not trust the usual pip-urls
    you can declare them with the option ``--trusted-host``,
-   e.g. ``pip install --trusted-host=pypi.python.org --trusted-host=pypi.org --trusted-host=files.pythonhosted.org -e .[develop]``
+   e.g. ``pip install --no-deps --trusted-host=pypi.python.org --trusted-host=pypi.org --trusted-host=files.pythonhosted.org -e .[develop]``
 -  Test that your installation was successful by running
    ``esmvaltool -h``.
 -  Install the :ref:`esmvaltool:pre-commit` hooks by running:

environment.yml

@@ -54,7 +54,7 @@ dependencies:
   - autodocsumm >=0.2.2
   - ipython <9.0  # github.com/ESMValGroup/ESMValCore/issues/2680
   - nbsphinx >=0.9.7  # github.com/ESMValGroup/ESMValCore/issues/2669
-  - 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 testing
   - pre-commit