ask per 2.13 release (#615)

2.13 release Co-authored-by: Romain Beucher <[email protected]>
underworldcode · Jun 8, 2022 · af142bb · af142bb
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -292,4 +292,4 @@ jobs:
         if: github.event_name == 'release'
         run: |
           pip install twine
-          python -m twine upload dist/* -r
+          python -m twine upload dist/* -r
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,24 +1,24 @@
 {
     "creators": [
         {
-            "name": "John Mansour",
-            "affiliation": "Monash eResearch Centre, Monash University",
-            "orcid": "0000-0001-5865-1664"
+            "name": "Romain Beucher",
+            "affiliation": "Research School of Earth Sciences, The Australian National University",
+            "orcid": "0000-0003-3891-5444"
         },
         {
             "name": "Julian Giordani",
-            "affiliation": "School of Earth Science, The University of Melbourne",
+            "affiliation": "School of Earth Science, The University of Sydney",
             "orcid": "0000-0003-4515-9296"
         },
         {
             "name": "Louis Moresi",
-            "affiliation": "Research School of Earth Sciences, The Australian National University; School of Earth Science, The University of Melbourne",
+            "affiliation": "Research School of Earth Sciences, The Australian National University",
             "orcid": "0000-0003-3685-174X"
         },
         {
-            "name": "Romain Beucher",
-            "affiliation": "School of Earth Science, The University of Melbourne",
-            "orcid": "0000-0003-3891-5444"
+            "name": "John Mansour",
+            "affiliation": "Monash eResearch Centre, Monash University",
+            "orcid": "0000-0001-5865-1664"
         },
         {
             "name": "Owen Kaluza",
@@ -43,7 +43,57 @@
             "name": "Adam Beall",
             "affiliation": "School of Earth and Ocean Sciences, Cardiff University",
             "orcid": "0000-0002-7182-1864"
-        }
+        },
+        {
+            "name": "Dan Sandiford",
+            "affiliation": "Monash University",
+            "orcid": "0000-0002-2207-6837"
+        },
+        {
+            "name": "Luke Mondy",
+            "affiliation": "School of Geosciences, Earthbyte Research Group, The University of Sydney",
+            "orcid": "0000-0001-7779-509X"
+        },
+        {
+            "name": "Claire Mallard", 
+            "affiliation": "School of Geosciences, Earthbyte Research Group, The University of Sydney",
+            "orcid": "0000-0003-2595-2414"
+        },      
+        {
+            "name": "Patrice Rey",
+            "affiliation": "School of Geosciences, Earthbyte Research Group, The University of Sydney",
+            "orcid": "0000-0002-1767-8593"
+        },      
+        {
+            "name": "Guillaume Duclaux",
+            "affiliation": "Laboratoire Géoazur, Université Nice Sophia Antipolis, Nice",
+            "orcid": "0000-0002-9512-7252"
+        },      
+        {
+            "name": "Arijit Laik", 
+            "affiliation": "Department of Earth Science, Faculty of Science, Vrije Universiteit",
+            "orcid": "0000-0002-3484-7985"
+        },      
+        {
+            "name": "Sara Morón",
+            "affiliation": "School of Geosciences, Earthbyte Research Group, The University of Sydney",
+            "orcid": "0000-0002-1270-4377"
+        },   
+        {
+            "name": "Adam Beall",
+            "affiliation": "School of Earth and Ocean Sciences, Cardiff University",
+            "orcid": "0000-0002-7182-1864"
+        },
+        {
+            "name": "Ben Knight",
+            "affiliation": "Monash University",
+            "orcid": "0000-0001-7919-2575"
+        },  
+        {
+            "name": "Neng Lu",
+            "affiliation": "Research School of Earth Sciences, The Australian National University",
+            "orcid": "0000-0001-9424-2315"
+        } 
     ],
     "license": "lgpl-3.0",
     "title": "Underworld2: Python Geodynamics Modelling for Desktop, HPC and Cloud",

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,10 +1,15 @@
 CHANGES: Underworld2
 =======================
-Release 2.13 [2022-05-30]
+
+Release 2.13-0 [2022-05-25]
+-----------------------------
 
 New:
- * UWGeodynamics (`from underworld import UWGeodynamics as GEO`) functionlity and models added. See https://www.underworldcode.org/articles/uwgeodynamics-and-underworld-merge/
--------------------
+ * Merge UWGeodynamics into Underworld (`from underworld import UWGeodynamics as GEO`)
+ * Compatibility with petsc 3.17.
+ * Update Docker images: Ubuntu 22.04LTS and mpich 4.0.2, python 3.10, petsc 3.17.1
+ * Update install_docs/nci gadi
+
 
 Release 2.12.0 [2022-01-31]
 ---------------------------

diff --git a/README.md b/README.md
@@ -54,9 +54,9 @@ Note that it can take a while for the site to fire up and that it will time-out
 
 | | |
 |-|-|
+| [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.13.0b) | v2.13.0b |
 | [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.12.0b) | v2.12.0b |
 | [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.11.0b) | v2.11.0b |
-| [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/v2.10.0b) | v2.10.0b |
 | [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/underworldcode/underworld2/development) | dev |
 
 

diff --git a/conda/LICENSE.md b/conda/LICENSE.md
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,17 +1,20 @@
-{% set name = "underworld2" %}
-{% set version = "2.10.0b" %}
+{% set name = "underworld" %}
+{% set version = "2.12.2" %}
+{% set sha256 = "5bbfa0b1ace0e5333cebd66c14828f235d728ac78249fec2281d104dc5c697b7" %}
+{% set build = 0 %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  path: ../.
+  url: https://github.com/underworldcode/underworld2/archive/refs/tags/v{{ version }}b.tar.gz
+  sha256: {{ sha256 }}
 
 build:
   skip: true  # [win]
   number: 0
-  script: {{ PYTHON }} -m pip install . -vv 
+  script: PETSC_DIR=$PREFIX {{ PYTHON }} -m pip -vv install --no-deps .  
   missing_dso_whitelist:
     - libm.so.6 
     - libc.so.6 
@@ -29,9 +32,9 @@ requirements:
     - pip
     - python
     - libxml2
-    - numpy>=1.18
+    - numpy >=1.18
     - cmake
-    - swig>=4.0.0
+    - swig >=4.0.0
     - ninja
     - petsc {{ petsc }}
     - {{ mpi }}
@@ -40,7 +43,7 @@ requirements:
     - python
     - {{ mpi }}
     - numpy
-    - petsc
+    - petsc {{ petsc }}
     - pint
     - scipy
     - mpi4py
@@ -73,6 +76,5 @@ about:
 extra:
   recipe-maintainers:
     - rbeucher
-    - jmansour
-    - jgiordani
+    - julesghub
     - lmoresi
diff --git a/docs/development/docker/docker.md b/docs/development/docker/docker.md
@@ -37,6 +37,14 @@ https://hub.docker.com/u/underworldcode/
 Releases
 -----------
 
+Note that because we cannot yet build ARM images automatically using github actions.
+We need to build and push them manually from the mac mini (M1) making sure that we properly tag and create the docker manifest.
+
+    ```
+    $ docker manifest create underworldcode/petsc --amend underworldcode/petsc:amd64 --amend underworldcode/petsc:arm64
+    $ docker manifest push underworldcode/petsc
+    ```
+
 Example, if `2.5` release:
 
 ** Tag the release locally:

diff --git a/docs/development/docker/petsc/Dockerfile b/docs/development/docker/petsc/Dockerfile
@@ -71,6 +71,7 @@ RUN ldconfig
 # create venv now for forthcoming python packages
 USER $NB_USER
 RUN /usr/bin/python3 -m virtualenv --system-site-packages --python=/usr/bin/python3 ${VIRTUAL_ENV}
+RUN pip3 install --no-cache-dir Cython git+https://github.com/mpi4py/[email protected]
 
 USER root
 # build petsc
@@ -79,8 +80,10 @@ ARG PETSC_VERSION="3.17.1"
 RUN wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${PETSC_VERSION}.tar.gz
 RUN tar zxf petsc-lite-${PETSC_VERSION}.tar.gz
 WORKDIR /tmp/petsc-build/petsc-${PETSC_VERSION}
+RUN python3 -m pip install cython
 RUN python3 ./configure --with-debugging=0 --prefix=/usr/local \
                 --COPTFLAGS="-g -O3" --CXXOPTFLAGS="-g -O3" --FOPTFLAGS="-g -O3" \
+                --with-petsc4py=1               \
                 --with-zlib=1                   \
                 --download-hdf5=1               \
                 --download-mumps=1              \
@@ -90,6 +93,9 @@ RUN python3 ./configure --with-debugging=0 --prefix=/usr/local \
                 --download-hypre=1              \
                 --download-scalapack=1          \
                 --download-superlu_dist=1       \
+                --download-ctetgen              \
+                --download-eigen                \
+                --download-triangle             \
                 --useThreads=0                  \
                 --download-superlu=1            \
                 --with-shared-libraries         \

diff --git a/docs/development/release_guidelines.md b/docs/development/release_guidelines.md
@@ -37,7 +37,7 @@ Documentation review
 	- review latest content
 * Review top level `README.md`.
 * Review `LICENSE.md`.
-* Review `.zenodo.json` (and validate using `jsonlint`).
+* Review `.zenodo.json` (and validate using `jsonlint`, https://jsonlint.com/).
 * Update the copyright information if necessary.
 * Add new Binder link, and keep link to old Binder.
 * Generate/update change log (`CHANGES.md`).
@@ -62,6 +62,8 @@ Testing
 
 Creating the release
 ====================
+
+* Tag the release in git.
 * Create the release from within Github.
 * Check `docker/docker.md` for docker image release information.
 * Add tagged documentation version at http://underworld2.readthedocs.io/