Merge branch 'develop' into 'main'

Release Version 0.0.1

See merge request ricos/machine_learning/phlower!18

.github/workflows/gh_pages.yml

@@ -0,0 +1,55 @@
+name: github pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build_docs:
+    runs-on: ubuntu-latest
+    container:
+        image: python:3.10-slim
+    steps:
+      - name: checkout
+        uses: actions/checkout@v1
+
+      - name: setup
+        shell: bash
+        run: |
+          apt update -y
+          apt install -y make git
+          pip install poetry
+          poetry config virtualenvs.in-project false
+          poetry install
+
+      - name: build_pages
+        shell: bash
+        run: |
+          make document
+          mkdir public
+          cp -r docs/build/html/* public/
+
+      - name: upload_artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: html_pages
+          path: public/ # or path/to/artifact
+
+  deploy_docs:
+    runs-on: ubuntu-latest
+    needs: build_docs
+    steps:
+
+      - name: download_artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: html_pages
+          path: public/
+
+      - name: deploy_pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: public
+          force_orphan: true

.gitignore

@@ -157,4 +157,11 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/
+
+# Editor Setting
+.vscode
+
+# data
+
+tests/data

.gitlab-ci.yml

@@ -3,13 +3,13 @@ stages:
   - deploy
 
 default:
-  image: python:3.11-slim
+  image: python:3.10-slim
   before_script:
     - apt update
     - apt install -y make
     - pip install poetry
     - poetry config virtualenvs.in-project false
-    - poetry install
+    - make dev-install
 
 lint:
   stage: test
@@ -21,7 +21,7 @@ lint:
 pytest:
   stage: test
   script:
-    - poetry run pytest tests --cov=src --cov-report term-missing
+    - make test
     - poetry run python3 -m coverage html -d coverage
     - poetry run python3 -m coverage xml
   coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
@@ -37,19 +37,27 @@ pytest:
     - no-gpu
     - GenuineIntel
 
+e2e_test:
+  stage: test
+  script:
+    - make e2e_test
+  tags:
+    - no-gpu
+    - GenuineIntel
 
-# pages:
-#   stage: deploy
-#   script:
-#     - make document
-#   artifacts:
-#     paths:
-#       - public
-#   only:
-#     - main
-#     - develop
-#     - fix_sphinx
-
+pages:
+  stage: deploy
+  script:
+    - make document
+    - mkdir public
+    - cp -r docs/build/html/* public/
+  artifacts:
+    paths:
+      - public
+  only:
+    - main
+    - develop
+    - fix_sphinx
 
 .deploy:wheel:
   stage: deploy

Makefile

@@ -1,3 +1,5 @@
+IN_PROJECT?=true
+
 
 .PHONY: init
 init:
@@ -6,42 +8,38 @@ init:
 	poetry install
 
 
-.PHONY: black-check
-black-check:
-	poetry run black --check src tests
-
-.PHONY: black
-black:
-	poetry run black src tests
-
-.PHONY: flake8
-flake8:
-	poetry run flake8 src tests
-
-.PHONY: isort-check
-isort-check:
-	poetry run isort --check-only src tests
-
-.PHONY: isort
-isort:
-	poetry run isort src tests
-
 .PHONY: mypy
 mypy:
 	poetry run mypy src
 
 .PHONY: format
 format:
-	$(MAKE) black
-	$(MAKE) isort
+	poetry run python3 -m ruff check --select I --fix
+	poetry run python3 -m ruff format
 
 .PHONY: test
 test:
-	poetry run pytest tests --cov=src --cov-report term-missing --durations 5
+	poetry run pytest tests -m "not e2e_test" --cov=src --cov-report term-missing --durations 5
+
+
+.PHONY: test
+e2e_test:
+	poetry run pytest tests -m "e2e_test"
+
 
 .PHONY: lint
 lint:
-	$(MAKE) black-check
-	$(MAKE) isort-check
-	$(MAKE) flake8
-	$(MAKE) mypy
+	poetry run python3 -m ruff check --diff
+	# $(MAKE) mypy
+
+.PHONY: dev-install
+dev-install: init
+	poetry run python3 -m pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
+
+
+.PHONY: document
+document:
+	rm -rf docs/build || true
+	rm -rf docs/source/reference/generated || true
+	rm -rf docs/source/tutorials/basic_usages || true
+	poetry run sphinx-build -M html docs/source docs/build

README.md

@@ -1,4 +1,29 @@
 # phlower
 
-This is a Python package which helps you handle GNN especially for physics problems.
+
+__phlower__ is a deep learning framework based on PyTorch especially for physical phenomenon such as fluid dynamics.
+
+For more details, please refer to user manual below.
+
+- [User Manual](https://ricosjp.github.io/phlower/)
+
+
+## Key Features
+
+
+Tutorials are prepared for key features !
+
+1. [Extended Tensor object which enables you to handle physics dimention](https://github.com/ricosjp/phlower/tutorials/basic_usages/01_phlower_tensor_basic)
+2. [Model definition by yaml file](https://github.com/ricosjp/phlower/tutorials/basic_usages/02_model_definition_by_yaml_file)
+3. [High Level API for scaling, training and predicion](https://github.com/ricosjp/phlower/tutorials/basic_usages/03_high_level_api_for_scaling_training_and_prediction)
+
+
+
+## Usage
+
+**phlower** can be installed with pip. Python 3.10 or newer is supported.
+
+```
+pip install phlower
+```
 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/.gitignore

@@ -0,0 +1,4 @@
+reference/generated
+tutorials/**
+!tutorials/index.rst
+sg_execution_times.rst

docs/source/_templates/autosummary/class.rst

@@ -0,0 +1,22 @@
+:orphan:
+
+{% extends "!autosummary/class.rst" %}
+
+{#
+Inherited methods from parent class are not shown in this manual.
+original templates are located in `.venv/lib/python3.10/site-packages/sphinx/ext/autosummary/templates/autosummary`
+#}
+{% block methods %}
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+   {% if item in inherited_members %}
+   {% else %}
+      ~{{ name }}.{{ item }}
+   {% endif %}
+   {%- endfor %}
+   {% endif %}
+
+{% endblock %}

docs/source/_templates/autosummary/nn.rst

@@ -0,0 +1,25 @@
+:orphan:
+
+{% extends "!autosummary/class.rst" %}
+
+{#
+Specific methods are only shown in this manual.
+showitems = ["from_setting", "get_nn_name", "forward"]
+original templates are located in `.venv/lib/python3.10/site-packages/sphinx/ext/autosummary/templates/autosummary`
+#}
+
+{% block methods %}
+   {% set showitems = ["from_setting", "get_nn_name", "forward"] %}
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+   {% if item not in showitems %}
+   {% else %}
+      ~{{ name }}.{{ item }}
+   {% endif %}
+   {%- endfor %}
+   {% endif %}
+
+{% endblock %}

docs/source/_templates/autosummary/settings.rst

@@ -0,0 +1,23 @@
+:orphan:
+
+{% extends "!autosummary/class.rst" %}
+
+{#
+Methods which startswith "model_" are not shown in this manual.
+original templates are located in `.venv/lib/python3.10/site-packages/sphinx/ext/autosummary/templates/autosummary`
+#}
+
+{% block methods %}
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+   {% if item.startswith("model_") %}
+   {% else %}
+      ~{{ name }}.{{ item }}
+   {% endif %}
+   {%- endfor %}
+   {% endif %}
+
+{% endblock %}