Merge remote-tracking branch 'upstream/develop' into gsoc-develop-merge

# Conflicts:
#	mslib/msui/_tests/test_mscolab.py
#	mslib/msui/_tests/test_mss_pyui.py
#	mslib/msui/mscolab.py

.github/workflows/testing.yml

@@ -39,7 +39,12 @@ jobs:
       run: |
         source /opt/conda/bin/activate mssenv \
         && cd $GITHUB_WORKSPACE \
-        && pytest --cov=mslib mslib
+        && pytest --cov=mslib mslib \
+        || (for i in {1..5} \
+          ; do pytest mslib --last-failed --lfnf=none \
+          && break \
+        ; done)
+
         
     - name: coveralls
       if: ${{ always() && github.event_name == 'push' && github.ref == 'refs/heads/develop' }}

.github/workflows/xdist_testing.yml

@@ -39,4 +39,8 @@ jobs:
       run: |
         source /opt/conda/bin/activate mssenv \
         && cd $GITHUB_WORKSPACE \
-        && pytest -n 6 --dist loadscope --max-worker-restart 0 mslib
+        && pytest -n 6 --dist loadscope --max-worker-restart 0 mslib \
+        || (for i in {1..5} \
+          ; do pytest -n 6 --dist loadscope --max-worker-restart 0 mslib --last-failed --lfnf=none \
+          && break \
+        ; done)

.gitignore

@@ -15,5 +15,8 @@ mslib/mswms/mss_wms_settings.py
 mslib/mswms/mss_wms_auth.py
 mslib/mscolab/colabdata/
 docs/_build
+docs/gallery/plots
+docs/gallery/code
+docs/gallery/plots.html
 build/
 mss.egg-info/

.readthedocs.yaml

@@ -0,0 +1,2 @@
+conda:
+  file: docs/environment.yml

AUTHORS

@@ -1,6 +1,8 @@
 Contributors
 ============
 
+in alphabetic order by first name
+
 
 - Andreas Hilboll <hilboll@uni-bremen.de>
 - Anveshan Lal <anveshanrx8@gmail.com>
@@ -10,10 +12,10 @@ Contributors
 - Jens-Uwe Grooß <j.-u.grooss@fz-juelich.de>
 - Jörn Ungermann <j.ungermann@fz-juelich.de>
 - Marc Rautenhaus <wxmetvis@posteo.de>
+- May Bär <m.baer@fz-juelich.de>
 - Reimar Bauer <rb.proj@gmail.com>
 - Sakshi Chopkar <sakshichopkar@gmail.com>
 - Shivashis Padhi <shivashispadhi@gmail.com>
 - Tanish Grover <tanish1908@gmail.com>
 - Thomas Breuer <t.breuer@fz-juelich.de>
 - Vaibhav Mehra <veb7vmehra@gmail.com>
-- May Bär <m.baer@fz-juelich.de>

CHANGES.rst

@@ -1,6 +1,30 @@
 Changelog
 =========
 
+Version 4.0.3
+~~~~~~~~~~~~~
+
+Bug fix release
+
+All changes:
+https://github.com/Open-MSS/MSS/milestone/62?closed=1
+
+Version 4.0.2
+~~~~~~~~~~~~~
+
+Bug fix release
+
+All changes:
+https://github.com/Open-MSS/MSS/milestone/60?closed=1
+
+Version 4.0.1
+~~~~~~~~~~~~~
+
+Bug Fix release
+
+All changes:
+https://github.com/Open-MSS/MSS/milestone/58?closed=1
+
 Version 4.0.0
 -------------
 

conftest.py

@@ -78,7 +78,7 @@ def pytest_generate_tests(metafunc):
     This file is part of mss.
 
     :copyright: Copyright 2019 Shivashis Padhi
-    :copyright: Copyright 2019-2020 by the mss team, see AUTHORS.
+    :copyright: Copyright 2019-2021 by the mss team, see AUTHORS.
     :license: APACHE-2.0, see LICENSE for details.
 
     Licensed under the Apache License, Version 2.0 (the "License");

docs/conf.py

@@ -12,7 +12,57 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 import os
+import sys
 import logging
+import setuptools
+import subprocess
+from string import Template
+
+if os.getenv("PROJ_LIB") is None or os.getenv("PROJ_LIB") == "PROJ_LIB":
+    conda_file_dir = setuptools.__file__
+    conda_dir = conda_file_dir.split('lib')[0]
+    proj_lib = os.path.join(os.path.join(conda_dir, 'share'), 'proj')
+    if "win" in sys.platform:
+        proj_lib = os.path.join(os.path.join(conda_dir, 'Library'), 'share')
+    os.environ["PROJ_LIB"] = proj_lib
+    if not os.path.exists(proj_lib):
+        os.makedirs(proj_lib)
+        epsg_file = os.path.join(proj_lib, 'epsg')
+        if not os.path.exists(epsg_file):
+            with open(os.path.join(proj_lib, 'epsg'), 'w') as fid:
+                fid.write("# Placeholder for epsg data")
+
+# Generate plot gallery
+import fs
+sys.path.insert(0, os.path.join(os.path.dirname(os.path.abspath(__file__)), ".."))
+from mslib.mswms.demodata import DataFiles
+
+root_fs = fs.open_fs("~/")
+if not root_fs.exists("mss/testdata"):
+    root_fs.makedirs("mss/testdata")
+
+examples = DataFiles(data_fs=fs.open_fs("~/mss/testdata"),
+                     server_config_fs=fs.open_fs("~/mss"))
+examples.create_server_config(detailed_information=True)
+examples.create_data()
+
+sys.path.insert(0, os.path.join(os.path.expanduser("~"), "mss"))
+
+import mslib.mswms.wms
+import mslib.mswms.gallery_builder
+
+# Generate template plots
+from docs.gallery.plot_examples import HS_template, VS_template
+dataset = [next(iter(mslib.mswms.wms.mss_wms_settings.data))]
+mslib.mswms.wms.mss_wms_settings.register_horizontal_layers = [(HS_template.HS_Template, dataset)]
+mslib.mswms.wms.mss_wms_settings.register_vertical_layers = [(VS_template.VS_Template, dataset)]
+mslib.mswms.wms.mss_wms_settings.register_linear_layers = []
+mslib.mswms.wms.server.__init__()
+mslib.mswms.wms.server.generate_gallery(sphinx=True, create=True, clear=True)
+mslib.mswms.gallery_builder.plots = {"Top": [], "Side": [], "Linear": []}
+
+# Generate all other plots
+mslib.mswms.wms.server.generate_gallery(sphinx=True, generate_code=True, all_plots=True)
 
 # readthedocs has no past.builtins
 try:
@@ -69,6 +119,21 @@
 # The full version, including alpha/beta/rc tags.
 release = __version__
 
+# Replace $variables in the .rst files if on a readthedocs worker
+if "/home/docs/checkouts" in " ".join(sys.argv):
+    mss_search = subprocess.run(["conda", "search", "-c", "conda-forge", "mss"], stdout=subprocess.PIPE,
+                                stderr=subprocess.STDOUT, encoding="utf8").stdout
+    # mss_search is inside a code block, reflect indentation
+    mss_search = (" " * 3).join([line for line in mss_search.splitlines(True) if line.startswith("mss ")][-2:])
+
+    for file in os.listdir():
+        if file.endswith(".rst"):
+            with open(file, "r") as rst:
+                content = Template(rst.read())
+            with open(file, "w") as rst:
+                rst.write(content.safe_substitute(mss_version=version[:-1] if version[-1] == "." else version,
+                                                  mss_search=mss_search))
+
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #

docs/development.rst

@@ -1,8 +1,8 @@
 .. _development:
 
-
+===========
 Development
-============================
+===========
 
 This chapter will get you started with MSS development.
 
@@ -30,13 +30,85 @@ Output and Logging
 When writing logger calls, always use correct log level (debug only for debugging, info for informative messages,
 warning for warnings, error for errors, critical for critical errors/states).
 
-Setup a development environment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Setting Up a Local Environment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-If you want to contribute make a fork on github of `MSS <https://github.com/Open-MSS/MSS>`_.
+Requirements
+------------
 
-In the mss package is some demodata included. The default where this is stored is $HOME/mss. Your clone of the
-MSS repository needs a different folder, e.g. workspace/mss. Avoid to mix data and source.
+1. System requirements
+
+  | Any system with basic configuration.
+  | Operating System : Any (Windows / Linux / Mac).
+
+2. Software requirement
+
+  | Python
+  | `Additional Requirements <https://github.com/Open-MSS/MSS/blob/develop/requirements.d/development.txt>`_
+
+
+3. Skill set
+
+  | Knowledge of git & github
+  | python
+
+Forking the Repo
+----------------
+
+1. Firstly you have to make your own copy of project. For that you have to fork the repository. You can find the fork button on the top-right side of the browser window.
+
+2. Kindly wait till it gets forked.
+
+3. After that copy will look like *<your-user-name>/MSS* forked from *Open-MSS/MSS*.
+
+Cloning the Repo
+----------------
+
+1. Now you have your own copy of project. Here you have to start your work.
+
+2. Go to desired location on your computer where you want to set-up the project.
+
+3. Right click there and click on git bash. A terminal window will pop up
+
+4. Click The big green button which says "Code". Copy the URL. `Like this <https://user-images.githubusercontent.com/71402528/122255281-9a855d80-ceeb-11eb-9f85-fed38db30562.png>`_
+
+5. Now Type the command ``git clone <your-fork-url>.git`` and hit enter.
+
+6. Wait for few seconds till the project gets copied
+
+  or simply head over here for `cloning a repository <https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/cloning-a-repository-from-github/cloning-a-repository>`_
+
+7. Add the path of your local cloned mss directory to $PYTHONPATH.
+
+Setting up a git remote
+-----------------------
+
+1. Now you have to set up remote repositories
+
+2. Type ``git remote -v`` in terminal to list remote connections to your repo.
+
+3. It will show something like this:
+
+  ``origin  https://github.com/<your-user-name>/MSS.git`` (fetch)
+
+  ``origin  https://github.com/<your-user-name>/MSS.git`` (push)
+
+4. Now type the command git remote add upstream ``https://github.com/Open-MSS/MSS.git`` this will set upstream as main directory
+
+5. Again type in command git remote -v to check if remote has been set up correctly
+
+6. It should show something like this :
+
+  ``origin  https://github.com/<your-user-name>/MSS.git`` (fetch)
+
+  ``origin  https://github.com/<your-user-name>/MSS.git`` (push)
+
+  upstream        ``https://github.com/Open-MSS/MSS.git`` (fetch)
+
+  upstream        ``https://github.com/Open-MSS/MSS.git`` (push)
+
+Installing dependencies
+-----------------------
 
 MSS is based on the software of the conda-forge channel located, so we have to add this channel to the default::
 
@@ -53,26 +125,54 @@ Create an environment and install the whole mss package dependencies then remove
 
   $ conda create -n mssdev mamba
   $ conda activate mssdev
-  $ mamba install mss --only-deps
+  $ mamba install mss=$mss_version --only-deps
 
 You can also use conda to install mss, but mamba is a way faster.
 Compare versions used in the meta.yaml between stable and develop branch and apply needed changes.
 
-Add the path of your local cloned mss directory to $PYTHONPATH.
+Pushing your changes
+--------------------
 
-For developer we provide additional packages for running tests, activate your env and run::
+1. Now you have made the changes, tested them and built them. So now it's time to push them.
+2. Goto your terminal and type git status and hit enter, this will show your changes from the files
+3. Then type in git add and hit enter, this will add all the files to staging area
+4. Commit the changes by ``git commit -m "<message-describing-your-change>"`` and hit enter.
+5. Now push your branch to your fork by ``git push origin <your-branch-name>`` and hit enter.
 
-  $ mamba install --file requirements.d/development.txt
 
-On linux install the `conda package pyvirtualdisplay` and `xvfb` from your linux package manager.
-This is used to run tests on a virtual display.
-If you don't want tests redirected to the xvfb display just setup an environment variable::
+Creating a pull request
+-----------------------
 
- $ export TESTS_VISIBLE=TRUE
+By this time you can see a message on your github fork as your fork is ahead of Open-MSS:develop by <number> of commits and also you can see a button called Compare and pull request.
+
+Click on Compare and pull request button.
+
+You will see a template.
+
+Fill out the template completely by describing your change, cause of change, issue getting fixed etc.
 
+After filling the template completely click on Pull request
+
+How to Report Bugs
+~~~~~~~~~~~~~~~~~~
+
+Please open a new issue in the appropriate GitHub repository `here <https://github.com/Open-MSS/MSS/issues/new>`_ with steps to reproduce the problem you're experiencing.
+
+Be sure to include as much information including screenshots, text output, and both your expected and actual results.
+
+How to Request Enhancements
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+First, please refer to the applicable `GitHub repository <https://github.com/Open-MSS/MSS>`_ and search `the repository's GitHub issues <https://github.com/Open-MSS/MSS/issues>`_ to make sure your idea has not been (or is not still) considered.
+
+Then, please `create a new issue <https://github.com/Open-MSS/MSS/issues/new>`_ in the GitHub repository describing your enhancement.
+
+Be sure to include as much detail as possible including step-by-step descriptions, specific examples, screenshots or mockups, and reasoning for why the enhancement might be worthwhile.
 
 Setup demodata
 ~~~~~~~~~~~~~~
+In the mss package is some demodata included. The default where this is stored is $HOME/mss. Your clone of the
+MSS repository needs a different folder, e.g. workspace/mss. Avoid to mix data and source.
 
 :ref:`demodata` is provided by executing::
 
@@ -104,6 +204,15 @@ Now you can use the MSS desktop application to connect to it using the Mscolab w
 
 Running tests
 ~~~~~~~~~~~~~~~~~~~
+For developers we provide additional packages for running tests, activate your env and run::
+
+  $ mamba install --file requirements.d/development.txt
+
+On linux install the `conda package pyvirtualdisplay` and `xvfb` from your linux package manager.
+This is used to run tests on a virtual display.
+If you don't want tests redirected to the xvfb display just setup an environment variable::
+
+ $ export TESTS_VISIBLE=TRUE
 
 We have implemented demodata as data base for testing. On first call of pytest a set of demodata becomes stored
 in a /tmp/mss* folder. If you have installed gitpython a postfix of the revision head is added.
@@ -190,7 +299,7 @@ If you don't have a stable branch, create one first or change to that branch::
 Merging stable into develop
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Bug fixes we have done in stable we need to merge regulary into develop too:: 
+Bug fixes we have done in stable we need to merge regulary into develop too::
 
    git checkout stable
    git pull git@github.com:Open-MSS/MSS.git stable
@@ -255,4 +364,3 @@ Publish on Conda Forge
 * rerender the feedstock by conda smithy
 * send a pull request
 * maintainer will merge if there is no error
-

docs/environment.yml

@@ -0,0 +1,26 @@
+channels:
+  - conda-forge
+  - default
+  - defaults
+dependencies:
+  - pip
+  - pip:
+      - flask
+      - flask-httpauth
+      - chameleon
+      - multidict
+      - isodate
+      - scipy
+      - metpy
+      - markdown
+      - xstatic
+      - defusedxml
+      - sphinx_rtd_theme
+      - sphinx
+      - fs
+      - netCDF4
+      - future
+      - pint
+      - PyQt5
+      - owslib
+  - basemap