Add poetry and update CI (#108)

* Install packages with poetry

* Add mongomock dev dependency

* Create initial GitHub Actions workflow

* Fix parser grammar weights

* Update pymongo insertion function

* Add poetry entrypoint for CLI

* Update pymongo update function

* Move contents of setup to pyproject

* Fix unit tests

* Remove travis config

* Update dependencies

* Update gitignore

---------

Co-authored-by: ElliottKasoar <[email protected]>

.github/workflows/ci.yml

@@ -0,0 +1,32 @@
+name: ci
+
+on: [push, pull_request]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install poetry
+      run: pipx install poetry
+
+    - name: Install python dependencies
+      run: |
+        poetry env use ${{ matrix.python-version }}
+        poetry install --with dev
+
+    - name: Run unit tests
+      run: |
+        poetry run python -m unittest -v tests
+

.gitignore

@@ -17,6 +17,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
@@ -31,6 +32,7 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+*.lock
 MANIFEST
 
 # PyInstaller

abcd/backends/atoms_pymongo.py

@@ -53,10 +53,11 @@ def _id(self):
 
     def save(self):
         if not self._id:
-            self._collection.insert(self)
+            self._collection.insert_one(self)
         else:
-            self._collection.update(
-                {"_id": ObjectId(self._id)}, self)
+            new_values = { "$set": self }
+            self._collection.update_one(
+                {"_id": ObjectId(self._id)}, new_values)
 
     def remove(self):
         if self._id:

abcd/parsers/extras.py

@@ -8,7 +8,7 @@
     key: NAME
     key_value: NAME "=" value
 
-    NAME.2: ("_"|LETTER|DIGIT) ("_"|"-"|LETTER|DIGIT)*  
+    NAME: ("_"|LETTER|DIGIT) ("_"|"-"|LETTER|DIGIT)*
 
     ?value: 
           | ESCAPED_STRING     -> string

pyproject.toml

@@ -0,0 +1,37 @@
+[tool.poetry]
+name = "abcd"
+version = "0.6.0"
+description = "This is a package which helps to store and share atomistic data."
+authors = ["Adam Fekete", "Gabor Csanyi"]
+keywords=["ase", "database", "mongo", "flask", "opensearch"]
+readme = "README.md"
+homepage = "https://libatoms.github.io/abcd/"
+repository = "https://github.com/libatoms/abcd"
+documentation = "https://libatoms.github.io/abcd/"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+notebook = "^7.2"
+numpy = "^1.26"
+tqdm = "^4.66"
+pymongo = "^4.7.3"
+matplotlib = "^3.9"
+ase = "^3.23"
+lark = "^1.1.9"
+
+[tool.poetry.group.dev.dependencies]
+mongomock = "^4.1.2"
+
+[tool.poetry.extras]
+tests = ["mongomock"]
+mongo = ["pymongo"]
+http = ["requests"]
+server-api = ["flask"]
+server-app = ["flask", "Flask-Nav", "Flask-MongoEngine", "gunicorn", "flask-paginate"]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.plugins."console_scripts"]
+"abcd" = "abcd.frontends.commandline:main"