Merge pull request #183 from MetOffice/develop

Update master for V1

.flake8

@@ -31,16 +31,17 @@ ignore = E123, E133, E226, W503, F405, E721, E402, F403, F401
 max-line-length = 88
 extend-ignore = E203
 
+
 count = True
-max-doc-length = 79
+max-doc-length = 88
 statistics = True
 doctests = True
 include_in_doctest =
     lib/catnip/preparation.py,
     lib/catnip/analysis.py,
     lib/catnip/utils.py
 
-exclude = 
+exclude =
     # ignore the following directories/files
     docs,
     docsrc,
@@ -52,3 +53,4 @@ exclude =
     *.pyc,
     runAll.py,
     testconf.py
+    setup.py

.github/workflows/tests.yml

@@ -0,0 +1,42 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    strategy:
+      matrix:
+        env: [current, next]
+    steps:
+    - uses: actions/checkout@v2
+    - name: update conda env
+      shell: bash
+      run: |
+        source '/usr/share/miniconda/etc/profile.d/conda.sh'
+        conda install -c conda-forge mamba
+        mamba env update -q --file envs/default-${{ matrix.env }}.yml --name default-${{ matrix.env }}
+    - name: conda info
+      run: |
+        source '/usr/share/miniconda/etc/profile.d/conda.sh'
+        conda activate default-${{ matrix.env }}
+        conda info
+        conda list
+    - name: pytest
+      run: |
+        source '/usr/share/miniconda/etc/profile.d/conda.sh'
+        conda activate default-${{ matrix.env }}
+        cd lib
+        pytest -p no:warnings -v
+    - name: flake8
+      run: |
+        source '/usr/share/miniconda/etc/profile.d/conda.sh'
+        conda activate default-${{ matrix.env }}
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exit-zero --max-complexity=10 --max-line-length=127
+    - name: Sphinx
+      run: |
+        source '/usr/share/miniconda/etc/profile.d/conda.sh'
+        conda activate default-${{ matrix.env }}
+        cd docsrc
+        make github

bin/run_all_tests.sh

@@ -13,7 +13,6 @@ export LC_CTYPE=en_GB.utf8
 
 FILES_TO_TEST=$(find $CATNIP_LIB_DIR -type f -name '*.py')
 
-
 function check_flake8 {
 	echo -e "\033[1;32mRunning flake8 tests ...\033[0m"
 	flake8
@@ -22,21 +21,77 @@ function check_flake8 {
 function check_black {
 	echo -e "\033[1;32mRunning black tests ...\033[0m"
 	module unload scitools
-	module load scitools/experimental-current
-        black $FILES_TO_TEST
+	#module load scitools/experimental-current
+	module load scitools/default-next
+  black $FILES_TO_TEST
 
 }
 
 function check_documentation {
 	echo -e "\033[1;32mChecking documentation ...\033[0m"
-	echo "TODO"
+	# Build documentation as test.
+	cd $CATNIP_ROOT_DIR/docsrc
+	make github
 }
 
 function check_license {
         echo -e "\033[1;32mChecking for license ...\033[0m"
-        echo "TODO"
+				# Iterate through files to check whether they contain the expected
+				# licence information. If any files do not contain the expected licence
+				# information, then this test will fail.
+read -d '' expected <<'__TEXT__' || true
+# -*- coding: utf-8 -*-
+# -----------------------------------------------------------------------------
+# (C) British Crown Copyright 2017-2020 Met Office.
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+__TEXT__
+
+
+      echo $FILES_TO_TEST
+			count=0
+			for FILE in $FILES_TO_TEST; do
+					# Check whether file has a size greater than zero.
+					echo 'Checking: ' $FILE
+					if [[ -s $FILE ]]; then
+							file_contents=$(<$FILE)
+							if [[ "$file_contents" != *"$expected"* ]]; then
+								echo 'Licence information is not found in ' $FILE
+								count=$((count+1))
+							fi
+					fi
+			done
+			if (( $count > 0 )); then
+					return 1
+			fi
 }
 
+
 function check_pytest {
 	echo -e "\033[1;32mRunning pytest ...\033[0m"
 	cd $CATNIP_LIB_DIR

docs/_sources/tools.rst.txt

@@ -4,7 +4,7 @@ analysis module
 .. toctree::
    :maxdepth: 2
 
-.. automodule:: catnip.analysis
+.. automodule:: analysis
     :members:
 
 preparation module
@@ -13,7 +13,7 @@ preparation module
 .. toctree::
    :maxdepth: 2
 
-.. automodule:: catnip.preparation
+.. automodule:: preparation
     :members:
 
 
@@ -23,7 +23,7 @@ visualisation module
 .. toctree::
    :maxdepth: 2
 
-.. automodule:: catnip.visualisation
+.. automodule:: visualisation
     :members:
 
 .. image:: images/regress_ci.png
@@ -38,5 +38,5 @@ utils module
 .. toctree::
    :maxdepth: 2
 
-.. automodule:: catnip.utils
+.. automodule:: utils
     :members: