update deps and conda spec file linux-64.spec

.github/workflows/main.yml

@@ -25,8 +25,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         # Install dependencies from the requirements.txt file in the root directory
-        pip install -r requirements.txt
+        pip install -r requirements.txt "pytest>=6,<9"
 
     - name: Run tests
       run: |
+        pytest -o addopts="" tests/test_dependencies.py -q
         pytest tests/test_wps_drought.py -s

MANIFEST.in

@@ -1,5 +1,7 @@
 include Makefile
 include *.txt
+include *.spec
+include environment.yml
 include *.rst
 include tox.ini
 recursive-include albatross *

docs/source/dev_guide.rst

@@ -35,7 +35,7 @@ First activate the ``albatross`` Conda environment and install ``pytest``.
 
 .. code-block:: console
 
-   $ source activate albatross
+   $ conda activate albatross
    $ pip install -r requirements_dev.txt  # if not already installed
    OR
    $ make develop
@@ -79,10 +79,16 @@ Update the Conda specification file to build identical environments_ on a specif
 .. code-block:: console
 
   $ conda env create -f environment.yml
-  $ source activate albatross
+  $ conda activate albatross
   $ make clean
   $ make install
-  $ conda list -n albatross --explicit > spec-file.txt
+  $ conda install -c conda-forge gunicorn gevent psycopg2=2.9.12 drmaa=0.7.9 dill pytest-cov
+  $ conda list -n albatross --explicit --md5 > linux-64.spec
+
+Include the current ``wps_conda_packages`` from the Ansible playbook before
+exporting; the command above reflects the deployment packages at this update.
+Commit ``linux-64.spec`` with any changes to ``environment.yml`` and
+``requirements.txt``.
 
 .. _environments: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#building-identical-conda-environments
 

docs/source/installation.rst

@@ -29,7 +29,7 @@ Create Conda environment named `albatross`:
 .. code-block:: console
 
    $ conda env create -f environment.yml
-   $ source activate albatross
+   $ conda activate albatross
 
 Install Albatross app:
 
@@ -108,6 +108,37 @@ Use Ansible to deploy Albatross on your System
 ----------------------------------------------
 
 Use the `Ansible playbook`_ for PyWPS to deploy Albatross on your system.
+The Linux x86_64 deployment environment is locked in ``linux-64.spec``. It
+includes the Conda runtime dependencies and the playbook's Gunicorn, gevent,
+psycopg2 2.9.12, DRMAA 0.7.9, dill and test packages.
+
+Set these inventory variables (including any overrides in ``etc/albatross_dkrz.yml``):
+
+.. code-block:: yaml
+
+   conda_env_use_spec: true
+   conda_env_spec_file: linux-64.spec
+
+The old ``spec-list.txt`` has been replaced. Run a full environment deployment
+so the updated packages are installed, rather than only updating application code.
+
+To install the same environment manually on Linux x86_64:
+
+.. code-block:: console
+
+   $ conda create -n albatross --file linux-64.spec
+   $ conda activate albatross
+   $ python -m pip install .
+
+Basemap 1.4.1, its data package and the compatible PyProj 3.6 wheel are
+installed by ``pip install .`` through ``requirements.txt``. Basemap and its
+data are not included in the Conda spec. Pip replaces the Conda PyProj package
+with the version required by Basemap. The pip wheel
+avoids the old Conda GEOS pin that conflicts with the deployment's GDAL stack.
+``environment.yml`` installs Basemap through its pip section as well.
+
+For other platforms, use ``environment.yml``. Both dependency definitions use
+Python 3.11 and PyWPS 4.7, preserving NumPy 1.x and Basemap 1.4 compatibility.
 
 
 .. _Ansible playbook: http://ansible-wps-playbook.readthedocs.io/en/latest/index.html

environment.yml

@@ -1,15 +1,28 @@
-name: nipa_env
+name: albatross
 channels:
   - conda-forge
-  - defaults
-  - anaconda
+  - nodefaults
 dependencies:
   - python=3.11
-  - pytest=8.3.5
-  - pydap
-  - numpy
-  - pandas
-  - matplotlib
   - pip
+  - click
+  - jinja2
+  - psutil
+  - pywps>=4.7,<4.8
+  # Preserve the Basemap 1.4 plotting stack used by the drought process.
+  - numpy>=1.26,<2
+  - pandas>=2.2,<3
+  - matplotlib-base>=3.8,<3.9
+  - pyshp>=2.3,<2.4
+  - packaging>=23,<24
+  # Basemap's Conda GEOS pin conflicts with the deployment's newer GDAL stack.
   - pip:
-      - -r file:requirements.txt
+      - basemap==1.4.1
+      - pyproj>=3.6,<3.7
+  - pydap>=3.5.4,<3.6
+  - scipy>=1.15,<2
+  - scikit-learn
+  - requests
+  - werkzeug
+  # tests
+  - pytest>=6,<9

requirements.txt

@@ -1,78 +1,13 @@
-alabaster==1.0.0
-asciitree==0.3.3
-attrs==25.3.0
-babel==2.17.0
+click
+jinja2
+psutil
+pywps>=4.7,<4.8
+numpy>=1.26,<2
+pandas>=2.2,<3
+matplotlib>=3.8,<3.9
 basemap==1.4.1
-basemap-data==1.3.2
-beautifulsoup4==4.13.3
-cattrs==24.1.2
-certifi==2025.1.31
-charset-normalizer==3.4.1
-click==8.1.8
-click-plugins==1.1.1
-cligj==0.7.2
-contourpy==1.3.1
-cycler==0.12.1
-Deprecated==1.2.18
-docutils==0.21.2
-fasteners==0.19
-fiona==1.10.1
-fonttools==4.56.0
-geotiff==0.2.10
-humanize==4.12.1
-idna==3.10
-imagesize==1.4.1
-iniconfig==2.0.0
-Jinja2==3.1.6
-jsonschema==4.23.0
-jsonschema-specifications==2024.10.1
-kiwisolver==1.4.8
-lxml==5.3.1
-MarkupSafe==3.0.2
-matplotlib==3.8.4
-mpl-tools==0.4.0
-numcodecs==0.15.1
-numpy==1.26.4
-OWSLib==0.32.1
-packaging==23.2
-pandas==2.2.3
-pillow==11.1.0
-platformdirs==4.3.6
-pluggy==1.5.0
-pydap==3.5.4
-Pygments==2.19.1
-pyparsing==3.2.1
-pyproj==3.6.1
-pyshp==2.3.1
-pytest==8.3.5
-python-dateutil==2.9.0.post0
-pytz==2025.1
-pywps==4.6.0
-PyYAML==6.0.2
-referencing==0.36.2
-requests==2.32.3
-requests-cache==1.2.1
-roman-numerals-py==3.1.0
-rpds-py==0.23.1
-scipy==1.15.2
-six==1.17.0
-snowballstemmer==2.2.0
-soupsieve==2.6
-Sphinx==8.2.3
-sphinxcontrib-applehelp==2.0.0
-sphinxcontrib-devhelp==2.0.0
-sphinxcontrib-htmlhelp==2.1.0
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==2.0.0
-sphinxcontrib-serializinghtml==2.0.0
-SQLAlchemy==2.0.39
-tifffile==2025.3.13
-typing_extensions==4.12.2
-tzdata==2025.1
-url-normalize==1.4.3
-urllib3==2.3.0
-WebOb==1.8.9
-Werkzeug==3.1.3
-wrapt==1.17.2
-zarr==2.12.0
+pydap>=3.5.4,<3.6
+scipy>=1.15,<2
 scikit-learn
+requests
+werkzeug

requirements_dev.txt

@@ -1,4 +1,4 @@
-pytest>=6.0
+pytest>=6,<9
 pytest-runner
 pytest-cov
 flake8

setup.py

@@ -9,15 +9,15 @@
 here = os.path.abspath(os.path.dirname(__file__))
 README = open(os.path.join(here, 'README.rst')).read()
 CHANGES = open(os.path.join(here, 'CHANGES.rst')).read()
-REQUIRES_PYTHON = ">=3.6.0"
+REQUIRES_PYTHON = ">=3.11,<3.12"
 
 about = {}
 with open(os.path.join(here, 'albatross', '__version__.py'), 'r') as f:
     exec(f.read(), about)
 
 setup_requirements = ['pytest-runner', ]
 
-test_requirements = ['pytest>=3', ]
+test_requirements = ['pytest>=6,<9', ]
 
 requirements = [line.strip() for line in open('requirements.txt')]
 
@@ -32,9 +32,7 @@
     'Programming Language :: Python',
     'Natural Language :: English',
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.5',
-    'Programming Language :: Python :: 3.6',
-    'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.11',
     'Topic :: Scientific/Engineering :: Atmospheric Science',
     'License :: OSI Approved :: Apache Software License',
 ]