Standalone parser with to json and back converters

.flake8

@@ -0,0 +1,14 @@
+[flake8]
+max-line-length = 88
+max-complexity = 16
+# B = bugbear
+# B9 = bugbear opinionated (incl line length)
+select = C,E,F,W,B,B9
+# E203: whitespace before ':' (black behaviour)
+# E501: flake8 line length (covered by bugbear B950)
+# W503: line break before binary operator (black behaviour)
+ignore = E203,E501,W503
+classmethod-decorators =
+    classmethod
+    validator
+exclude = pytopas/lark_standalone.py

.github/dependabot.yml

@@ -0,0 +1,12 @@
+---
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/linter.yml

@@ -0,0 +1,54 @@
+---
+# yamllint disable rule:line-length
+name: Lint Code Base
+
+on: # yamllint disable-line rule:truthy rule:comments
+  # allow this workflow to be called from other workflows
+  workflow_call:
+
+jobs:
+  lint:
+    name: Lint Code Base
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        if: ${{ !env.ACT }} # skip during local actions testing
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[lint,test]
+
+      - name: Autoflake
+        run: autoflake -c -r pytopas tests examples
+
+      - name: Black
+        run: black --check --diff .
+
+      - name: isort
+        run: isort -c --diff .
+
+      - name: flake8
+        run: flake8
+
+      - name: pylint
+        run: pylint .
+
+      - name: pyupgrade
+        run: |
+          find -name "*.py" -and -not -name "lark_standalone.py" -print0 |\
+          xargs -0 -n1 pyupgrade --py38-plus

.github/workflows/pr.yml

@@ -0,0 +1,39 @@
+---
+# yamllint disable rule:line-length
+name: PR action
+
+on:
+  pull_request:
+    types: [opened, reopened, synchronize]
+
+jobs:
+  lint:
+    uses: ./.github/workflows/linter.yml
+
+  test:
+    uses: ./.github/workflows/test.yml
+
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    needs: test
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        if: ${{ !env.ACT }} # skip during local actions testing
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev,release]
+
+      - name: Build
+        run: make dist

.github/workflows/push.yml

@@ -0,0 +1,75 @@
+---
+# yamllint disable rule:line-length
+name: Push action
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  test:
+    uses: ./.github/workflows/test.yml
+
+  release:
+    name: Bump version and create draft release
+    runs-on: ubuntu-latest
+    needs: test
+    permissions:
+      contents: write
+    concurrency:
+      group: release
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        if: ${{ !env.ACT }} # skip during local actions testing
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[release]
+
+      - name: Create bump and changelog
+        id: cz
+        if: github.repository == 'metis-science/pytopas'
+        uses: commitizen-tools/commitizen-action@4498afe6f2f1c5993fb29f22db7b597538c00aae
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          changelog_increment_filename: .CHANGELOG-CURRENT.md
+          push: true
+          commit: true
+
+      - name: Print new version
+        if: github.repository == 'metis-science/pytopas'
+        run: echo "Bumped to version ${{ steps.cz.outputs.version }}"
+
+      - name: Build
+        run: make dist
+
+      - name: Stop if no bump
+        id: no-bump
+        continue-on-error: true
+        # will fail if not on exact tag
+        run: git describe --tags --exact-match
+
+      - name: Create Release Draft
+        uses: softprops/action-gh-release@c9b46fe7aad9f02afd89b12450b780f52dacfb2d
+        if: steps.no-bump.outcome == 'success'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          draft: true
+          tag_name: v${{ steps.cz.outputs.version }}
+          body_path: .CHANGELOG-CURRENT.md
+          fail_on_unmatched_files: true
+          files: dist/*

.github/workflows/release.yml

@@ -0,0 +1,42 @@
+---
+# yamllint disable rule:line-length
+name: Publish release to pypi
+
+on:
+  release:
+    types: [published]
+
+  workflow_dispatch:
+
+jobs:
+  pypi:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: release
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        if: ${{ !env.ACT }} # skip during local actions testing
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[release]
+
+      - name: Build
+        run: make dist
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -0,0 +1,49 @@
+---
+# yamllint disable rule:line-length
+name: Run tests
+
+on: # yamllint disable-line rule:truthy rule:comments
+  # allow this workflow to be called from other workflows
+  workflow_call:
+
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        if: ${{ !env.ACT }} # skip during local actions testing
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[test]
+
+      - name: Run tests
+        run: |
+          pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v3
+        # Use always() to always run this step to publish test results
+        # when there are test failures
+        if: always()
+        with:
+          name: pytest-results-${{ matrix.python-version }}
+          path: junit/test-results-${{ matrix.python-version }}.xml

.gitignore

@@ -0,0 +1,8 @@
+*.log
+.CHANGELOG-CURRENT.md
+.DS_Store
+.coverage
+.idea
+dist/
+private_examples/
+tmp/

Makefile

@@ -0,0 +1,10 @@
+.DEFAULT_GOAL := parser
+.PHONY: parser
+
+pytopas/lark_standalone.py: pytopas/grammar.lark
+	PYTHONHASHSEED=0 python -m lark.tools.standalone -s topas $< > $@
+
+parser: pytopas/lark_standalone.py
+
+dist: pytopas/* pyproject.toml
+	flit build

README.md

@@ -0,0 +1,65 @@
+# pytopas
+
+Bruker's TOPAS macro language parser.
+
+## Usage
+
+Parse TOPAS source code and convert it to json:
+
+```python
+from pytopas import TOPASParser
+
+src = "a = a + 1 ; 0"
+
+parser = TOPASParser()
+tree = parser.parse(src)
+print(tree.to_json(compact=True))
+```
+
+Convert JSON encoded TOPAS code back into TOPAS source code:
+
+```python
+from pytopas import TOPASParseTree
+
+input_json = '["topas", ["a = a + 1 ; 0"]]'
+
+tree = TOPASParseTree.from_json(input_json)
+print(tree.to_topas())
+
+```
+
+## Command line utilities
+
+After installing the package, two command line utilities will be available.
+
+```
+usage: topas2json [-h] [-c] file
+
+Parse TOPAS input and output JSON
+
+positional arguments:
+  file           Path to TOPAS file or '-' for stdin input
+
+options:
+  -h, --help     show this help message and exit
+  -c, --compact  Use compact output
+```
+
+```
+usage: json2topas [-h] file
+
+Parse JSON input and output TOPAS
+
+positional arguments:
+  file        Path to JSON file or '-' for stdin input
+
+options:
+  -h, --help  show this help message and exit
+
+```
+
+## Development
+
+Install package with optional dependencies: `pip install -e .[dev,lint,test,release]`
+
+Regenerate standalone `lark` parser after `grammar.lark` change: `make parser`