Merge pull request #562 from MiraGeoscience/release/0.10.0

Release/0.10.0

.github/workflows/create_env_file.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: windows-latest
     env:
       releaseFullEnv: false
-      python_ver: '3.9'
+      python_ver: '3.10'
       PYTHONUTF8: 1
       ARTIFACT_NAME: geoapps.conda-env
       CONDA_ENV_FILE_GLOB_PATTERN: conda-py-*-geoapps*.lock.yml
@@ -27,8 +27,6 @@ jobs:
       artifact: ${{ env.ARTIFACT_NAME }}.${{ steps.git-info.outputs.git_ref_suffix }}
     steps:
       - uses: actions/checkout@v3
-        with:
-          lfs: true
       - name: git info
         id: git-info
         run: |

.github/workflows/issue_to_jira.yml

@@ -19,7 +19,7 @@ jobs:
         JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
     - name: Jira Create issue
       id: create_jira_issue
-      uses: atlassian/gajira-create@v2.0.1
+      uses: atlassian/gajira-create@v3.0.1
       with:
         project: GEOPY
         issuetype: Story

.github/workflows/pytest-unix-os.yaml

@@ -16,6 +16,10 @@ on:
       - feature/**
       - hotfix/**
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
 env:
   source_dir: geoapps
 
@@ -36,6 +40,8 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.lock.yml
     steps:
       - uses: actions/checkout@v3
+        with:
+          lfs: true
       - name: Setup conda env
         uses: mamba-org/provision-with-micromamba@main
         with:

.github/workflows/pytest-windows.yaml

@@ -16,6 +16,10 @@ on:
       - feature/**
       - hotfix/**
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
 env:
   source_dir: geoapps
 
@@ -35,6 +39,8 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-win-64-dev.lock.yml
     steps:
       - uses: actions/checkout@v3
+        with:
+          lfs: true
       - name: Setup conda env
         uses: mamba-org/provision-with-micromamba@main
         with:

.github/workflows/static-analysis.yml

@@ -16,6 +16,10 @@ on:
       - feature/**
       - hotfix/**
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
 env:
   source_dir: geoapps
 

.gitignore

@@ -142,13 +142,13 @@ get_custom_conda.bat
 
 # cleanup after tests
 *.lock
-/assets/EM1DInversion_.json
-/assets/Inversion_.json
-/assets/SimPEG_PFInversion/
-/assets/Temp/
-/assets/dask-worker-space/
-/assets/sensitivity/
-/assets/test_*
+/geoapps-assets/EM1DInversion_.json
+/geoapps-assets/Inversion_.json
+/geoapps-assets/SimPEG_PFInversion/
+/geoapps-assets/Temp/
+/geoapps-assets/dask-worker-space/
+/geoapps-assets/sensitivity/
+/geoapps-assets/test_*
 /tests/**/*ui.json
 /tests/GEOSCIENCEtemp
 /tests/Gravity*

.pre-commit-config.yaml

@@ -13,12 +13,9 @@ ci:
 repos:
 -   repo: https://github.com/psf/black
     rev: 23.3.0
+
     hooks:
     -   id: black
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
-    hooks:
-        -   id: seed-isort-config
 -   repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
@@ -34,6 +31,7 @@ repos:
 #    -   id: flake8
 -   repo: https://github.com/asottile/pyupgrade
     rev: v3.3.2
+
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
@@ -51,15 +49,17 @@ repos:
         language: system
         require_serial: true  # pylint does its own parallelism
         types: [python]
-        exclude: (devtools|docs)/
+        exclude: docs/
     -   id: check-copyright
         name: Check copyright
         entry: python devtools/check-copyright.py
         language: python
-        types: [python]
-        exclude: (^setup.py$|(docs|assets)/)
+        files: (^LICENSE|README.rst|\.py|\.pyi)$
+        types: [text]
+        exclude: (^setup.py$|^\.|\b(docs|geoapps-assets)/)
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.4
+
     hooks:
     -   id: codespell
         exclude: (-lock\.ya?ml|\benvironments/.*\.ya?ml|\.ipynb)$
@@ -82,6 +82,7 @@ repos:
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
     rev: v6.1.2
+
     hooks:
     -   id: rstcheck
         additional_dependencies: [sphinx]

Install_or_Update.bat

@@ -7,16 +7,32 @@ if !errorlevel! neq 0 (
   exit /B !errorlevel!
 )
 
-set PY_VER=3.9
+set PY_VER=3.10
 
+set ENV_NAME=geoapps
 set MY_CONDA=!MY_CONDA_EXE:"=!
 cd %~dp0
 set PYTHONUTF8=1
-call "!MY_CONDA!" activate
-call conda remove --name geoapps --all --yes
-call conda env create -f environments\conda-py-%PY_VER%-win-64.lock.yml -n geoapps
-call conda activate geoapps
-pip install -e . --no-deps
+
+:: all dependencies are installed from conda
+set PIP_NO_DEPS=1
+
+set MY_CONDA_ENV_FILE=environments\conda-py-%PY_VER%-win-64.lock.yml
+if not exist %MY_CONDA_ENV_FILE% (
+  echo "** ERROR: Could not find the conda environment specification file '%MY_CONDA_ENV_FILE%' **"
+  pause
+  exit /B 0
+)
+
+call "!MY_CONDA!" activate base ^
+  && call "!MY_CONDA!" env create --force -n %ENV_NAME% --file %MY_CONDA_ENV_FILE% ^
+  && call "!MY_CONDA!" run -n %ENV_NAME% pip install -e .[core,apps]
+
+if !errorlevel! neq 0 (
+  echo "** ERROR: Installation failed **"
+  pause
+  exit /B !errorlevel!
+)
 
 pause
-cmd /k
+cmd /k "!MY_CONDA!" activate base

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Mira Geoscience
+Copyright (c) 2023 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -0,0 +1,91 @@
+|coverage| |precommit_ci| |docs| |style| |version| |pyversions|
+
+
+.. |docs| image:: https://readthedocs.org/projects/geoapps/badge/
+    :alt: Documentation Status
+    :target: https://geoapps.readthedocs.io/en/latest/?badge=latest
+
+.. |coverage| image:: https://codecov.io/gh/MiraGeoscience/geoapps/branch/main/graph/badge.svg
+    :alt: Code coverage
+    :target: https://codecov.io/gh/MiraGeoscience/geoapps
+
+.. |style| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :alt: Coding style
+    :target: https://github.com/pf/black
+
+.. |version| image:: https://img.shields.io/pypi/v/geoapps.svg
+    :alt: version on PyPI
+    :target: https://pypi.python.org/pypi/geoapps/
+
+.. |pyversions| image:: https://img.shields.io/pypi/pyversions/geoapps.svg
+    :alt: Python versions
+    :target: https://pypi.python.org/pypi/geoapps/
+
+.. |precommit_ci| image:: https://results.pre-commit.ci/badge/github/MiraGeoscience/geoapps/main.svg
+    :target: https://results.pre-commit.ci/latest/github/MiraGeoscience/geoapps/main
+    :alt: pre-commit.ci status
+
+
+Welcome to **geoapps** - Open-source applications in geosciences
+================================================================
+
+.. image:: https://github.com/MiraGeoscience/geoapps/raw/v0.10.0-rc.3/docs/images/index_page.png
+    :align: right
+    :width: 50%
+
+In short
+^^^^^^^^
+
+The **geoapps** project has been created by `Mira Geoscience`_ for the development and sharing of open-source
+applications in geoscience. Users will be able to directly leverage the powerful visualization capabilities of
+`Geoscience ANALYST`_ along with open-source code from the Python ecosystem.
+
+.. _Mira Geoscience: https://mirageoscience.com/
+.. _Geoscience ANALYST: https://mirageoscience.com/mining-industry-software/geoscience-analyst/
+
+
+Links
+^^^^^
+
+- `Download the latest <https://github.com/MiraGeoscience/geoapps/archive/main.zip>`_
+- `Getting started <https://geoapps.readthedocs.io/en/latest/content/installation.html#installation>`_
+- `Documentation <https://geoapps.readthedocs.io/en/latest/index.html>`_
+
+
+Current sponsors
+^^^^^^^^^^^^^^^^
+
+- `Anglo American <http://www.angloamerican.ca/>`_
+- `Barrick <https://www.barrick.com/English/home/default.aspx>`_
+- `BHP <https://www.bhp.com/>`_
+- `Cameco <https://www.cameco.com/>`_
+- `Glencore <https://www.glencore.com/>`_
+- `Mira Geoscience`_
+- `Rio Tinto <https://www.riotinto.com/en>`_
+- `Teck <https://www.teck.com/>`_
+- `Vale <https://www.vale.com/canada>`_
+
+
+License
+^^^^^^^
+MIT License
+
+Copyright (c) 2023 Mira Geoscience
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Start_applications.bat

@@ -7,6 +7,8 @@ if !errorlevel! neq 0 (
   exit /B !errorlevel!
 )
 
+set ENV_NAME=geoapps
+
 set MY_CONDA=!MY_CONDA_EXE:"=!
-call "!MY_CONDA!" activate geoapps && jupyter notebook geoapps\index.ipynb
-cmd /k
+call "!MY_CONDA!" run --live-stream -n %ENV_NAME% python -m geoapps.scripts.start_notebook
+cmd /k "!MY_CONDA!" activate %ENV_NAME%