Merge pull request #499 from underworldcode/v2.10_release

V2.10 release
underworldcode · Aug 7, 2020 · 12161b5 · 12161b5
2 parents c37cf9b + 3514ca7
commit 12161b5
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,12 +1,34 @@
 CHANGES: Underworld2
 =======================
 
+Release 2.10.0 []
+----------------
+Fixes:
+* SWIG4 compatibility changes.
+* libxml2 ubuntu20.04 changes.
+* Numpy 1.19 compatability changes.
+* Fix `LGPLv3.txt` contents. File incorrect contained
+  GPLv3 text. 
+
+Changes:
+* Check for compressibility/penalty clash. 
+* Update example models for parallel usage. 
+
+New:
+* Add Dockerfile for Deepnote.
+* Add `test_long.sh` long test runner.
+
+Release 2.9.5 [2020-07-27]
+---------------------------
+Changes:
+* Fix `LGPLv3.txt` contents. File incorrect contained
+  GPLv3 text.
+
 Release 2.9.4 [2020-03-26]
 ---------------------------
 Changes:
 * Updating Dockerfile to include UWGeodynamics-2.9.4.
 
-
 Release 2.9.3 [2020-03-09]
 ---------------------------
 Changes:

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM underworldcode/underworld2:2.9.1b
+FROM underworldcode/underworld2:2.10.0b
 
 # Set the UW_MACHINE env variable for metrics
 ENV UW_MACHINE binder
diff --git a/LGPLv3.txt b/LGPLv3.txt
diff --git a/README.md b/README.md
@@ -5,7 +5,6 @@ Underworld 2
 
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.01797/status.svg)](https://doi.org/10.21105/joss.01797)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1436039.svg)](https://doi.org/10.5281/zenodo.1436039)
-[![Build Status](http://115.146.85.138:32779/buildStatus/icon?job=Underworld2%2Fdevelopment)](http://115.146.85.138:32779/job/Underworld2/job/development/)
 [![Docs Status](https://readthedocs.org/projects/underworld2/badge/?version=latest)](https://underworld2.readthedocs.io/en/latest/?badge=latest)
 [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/master)
 
@@ -34,6 +33,7 @@ You can try out the code immediately via a Jupyter Binder cloud instance. Be awa
 
 | | |
 |-|-|
+| [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.10.0b) | v2.10.0b (Py3) |
 | [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.9.2b) | v2.9.2b (Py3) |
 | [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.8.2b) | v2.8.2b (Py3) |
 | [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.7.1b) | v2.7.1b (Py2) |
@@ -65,11 +65,9 @@ Note that basic usage metrics are dispatched when you use Underworld. To opt out
 
 Licensing
 ---------
-Underworld is an open-source project licensed under LGPL-3. See `LICENSE.md` for details.
+Underworld is an open-source project licensed under LGPL Version 3. See `LICENSE.md` and `LGPLv3.txt` for details.
 
-Security Notice 
----------------
-Earlier versions of our Docker images disabled token authentication for Jupyter Notebook. This potentially left the user's container vulnerable, in particular where running on institution networks. All Docker images have now been updated to enable token authentication. Please ensure you are using an updated image by running `docker pull` for your given Underworld version (or better yet, updating to the latest release).
+Note that for releases `2.9.0`, `2.9.1`, `2.9.2`, `2.9.3` and `2.9.4`, the incorrect text was erroneously included within `LGPLv3.txt`, although these releases must still to be considered as licensed under LGPL Version 3.
 
 Citing Underworld
 -----------------

diff --git a/docs/development/docker/deepnote/Dockerfile b/docs/development/docker/deepnote/Dockerfile
@@ -0,0 +1,12 @@
+FROM gcr.io/deepnote-200602/templates/deepnote
+
+RUN sudo apt-get update -qq
+RUN DEBIAN_FRONTEND=noninteractive sudo apt-get install -yq --no-install-recommends bash-completion build-essential git python3-minimal python3-dev python3-pip libxml2-dev xorg-dev ssh curl libfreetype6-dev libpng-dev libxft-dev xvfb freeglut3 freeglut3-dev libgl1-mesa-dri libgl1-mesa-glx python3-tk rsync vim less xauth swig gdb python3-dbg cmake python3-setuptools wget ca-certificates gfortran petsc-dev
+
+RUN pip3 install --no-cache-dir packaging h5py appdirs numpy plotly matplotlib pillow pyvirtualdisplay ipython ipyparallel pint sphinx sphinx_rtd_theme sphinxcontrib-napoleon mock scipy tabulate mpi4py scons
+RUN pip3 install lavavu
+RUN pip3 install git+https://github.com/underworldcode/underworld2
+RUN pip3 install UWGeodynamics
+
+#  hack to force xvfb
+RUN sed -i 's/in _os/not in _os/g' /opt/venv/lib/python3.7/site-packages/underworld/visualisation/__init__.py
diff --git a/docs/development/guidelines.md b/docs/development/guidelines.md
@@ -48,7 +48,7 @@ Version Control
 We follow the Gitflow Workflow:
 https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow/
 
-Features branches should be created for anything besides quick fixes. Once ready for
+Features branches must be created for all changes. Once ready for
 publishing to the development branch, a pull request should be created and another
 team member nominated to review the changes. Pull request should only be merged
 once the following criterion are met:

diff --git a/docs/development/release_guidelines.md b/docs/development/release_guidelines.md
@@ -27,17 +27,19 @@ Documentation review
 * Review docstrings updates for deprecation warnings.
 * Check for other DEPRECATE flags in the code.
 * Check autocomplete to ensure no garbage has slipped in. Non
-   user relevant objects should be made private so they don't appear in
-   autocomplete suggestions.
+  user relevant objects should be made private so they don't appear in
+  autocomplete suggestions.
 * Review ``docs/`` for style, relevance and updates.
+* Review ``docs/install_guides``, in particular ensure that guides 
+  for Gadi & Magnus are up to date.
 * Review docs generated at http://underworld2.readthedocs.io/
 	- make sure builds are passing
 	- review latest content
 * Review top level `README.md`.
 * Review `LICENSE.md`.
-* Review `.zenodo.json`.
+* Review `.zenodo.json` (and validate using `jsonlint`).
 * Update the copyright information if necessary.
-** Add new Binder link, and keep link to old Binder.
+* Add new Binder link, and keep link to old Binder.
 * Generate/update change log (`CHANGES.md`).
 * Review cheat sheet contents.
 * Increment version number within ``underworld/_version.py``
@@ -46,18 +48,17 @@ Documentation review
 
 Testing
 =======
-* Ensure 'run_tests.py' script run to completion without raising an exception.
-* Test on
-** docker
-** OSX
-** linux
-** NCI
-** Pawsey
-* Scaling tests on NCI and Pawsey machines.
-* High resolution production tests on Raijin, Magnus run to completion with 
-  correct results.
-* Ensure jenkins and docker are working correctly.
-* Ensure metrics are being dispatched.
+* Ensure 'test_long.py' script run to completion without raising an exception.
+  Test on Docker/NCI/Pawsey. Note that parallel jobs within script may need to be
+  executed by hand on NCI/Pawsey.
+* Large parallel tests (NCI/Pawsey).
+  Compare against previous for timing performance, and confirming expected convergence rates for SolDB3d.
+  - IO=0, JOBS="1 2 4 6 8 10 12 14 16 18 20 24", BASE=16, ORDER=2, RTOL=1e-11, PENALTY=-1, MODEL=SOLDB3d
+  - IO=0, JOBS="1 2 4 6 8 10 12 14 16 18 20 24", BASE=32, ORDER=1, RTOL=1e-6,  PENALTY=-1, MODEL=SOLH
+  - IO=1, JOBS="1 2 4 6 8 10",                   BASE=32, ORDER=1, RTOL=1e-6,  PENALTY=-1, MODEL=SOLH
+* Confirm Jenkins is running tests and tests are returning expected results. 
+* Confirm Docker images are being generated correctly.
+* Confirm metrics are being dispatched.
 
 Creating the release
 ====================
@@ -74,6 +75,7 @@ Announce new version
 After the release
 ============
 * Increment version number within ``underworld/_version.py`` on dev branch (eg 2.6.0-dev)
+* Update `FROM` tag in top level (binder) Dockerfile to use dev images.
 * Check `docker/docker.md` for docker related actions.
 
 
diff --git a/docs/development/run_tests.py b/docs/development/run_tests.py
@@ -155,7 +155,7 @@ def run_file(fname, dir, exe, job):
        os.mkdir(dir)
 
     # create test log file
-    logFileName = "testing.log"
+    logFileName = "test_run.log"
     logFile = open(dir+logFileName, "w")
 
     maxjobs = args.jobs
@@ -179,7 +179,7 @@ def run_file(fname, dir, exe, job):
         # if prefix args found and it's an ipynb, use 'jupyter nbconvert --execute'
         if is_ipynb and not args.prepend:
             exe = ['jupyter', 'nbconvert', '--ExecutePreprocessor.kernel_name="python3"',
-                   '--ExecutePreprocessor.timeout=360','--execute', '--stdout']
+                   '--ExecutePreprocessor.timeout=10000','--execute', '--stdout']
         elif is_ipynb and args.prepend:
             # convert ipynb to py and run with python
             print("Converting test {} to .py".format(fname));

diff --git a/docs/examples/02_Convection_Example.ipynb b/docs/examples/02_Convection_Example.ipynb
@@ -358,7 +358,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.3"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/03_BlankenbachBenchmark.ipynb b/docs/examples/03_BlankenbachBenchmark.ipynb
diff --git a/docs/examples/04_StokesSinker.ipynb b/docs/examples/04_StokesSinker.ipynb
diff --git a/docs/examples/05_Rayleigh_Taylor.ipynb b/docs/examples/05_Rayleigh_Taylor.ipynb
diff --git a/docs/examples/06_SlabSubduction.ipynb b/docs/examples/06_SlabSubduction.ipynb
diff --git a/docs/examples/07_ShearBandsPureShear.ipynb b/docs/examples/07_ShearBandsPureShear.ipynb