Refactor the project organisation (#97)

* Start refactoring F2D

* Add more refactoring

* Move secondary files to tools/ + run black & isort

* Run flake8

* Move progressbar to a dedicated file + do more housekeeping

* Add tests for api call and request

* Update README

* Improve Parser and tests

* Improve GraphQuery and add tests

* Small fixes

Author: LaRiffle

.github/workflows/lint_and_test.yml

@@ -3,30 +3,30 @@ name: fhir2dataset
 on: [push]
 
 jobs:
-    build:
-        name: Lint and test
-        runs-on: ubuntu-18.04
-        strategy:
-            matrix:
-                python-version: ["3.6", "3.7","3.8"]
+  build:
+    name: Lint and test
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: ["3.6", "3.7", "3.8"]
 
-        steps:
-            - uses: actions/checkout@v2
-            - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v2
-              with:
-                  python-version: ${{ matrix.python-version }}
-            - name: Install dependencies
-              run: |
-                  python -m pip install --upgrade pip
-                  pip install -r requirements.txt
-                  pip install -r requirements-dev.txt
-                  npm install --prefix ./fhir2dataset/metadata
-            - name: Lint with flake8
-              run: |
-                  # stop the build if there are Python syntax errors or undefined names
-                  flake8 fhir2dataset --count --select=E9,F63,F7,F82 --show-source --statistics
-                  flake8 fhir2dataset --count --max-complexity=10 --max-line-length=100 --statistics
-            - name: Test with pytest
-              run: |
-                  python -m pytest -svv --log-level=DEBUG
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+          npm install --prefix ./fhir2dataset/metadata
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 fhir2dataset --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 fhir2dataset --count --max-line-length=100 --statistics
+      - name: Test with pytest
+        run: |
+          python -m pytest -svv --log-level=DEBUG

.pre-commit-config.yaml

@@ -1,24 +1,40 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.3.0
+    hooks:
+      - id: check-added-large-files # Prevent giant files from being committed
+      - id: check-ast # Check whether the files parse as valid python
+      - id: check-json # Check json files for parseable syntax
+      - id: check-merge-conflict # Check for files that contain merge conflict strings
+      - id: check-toml # Checks toml files for parseable syntax
+      - id: check-yaml # Check yaml files for parseable syntax
+      - id: debug-statements # Check for debugger imports and `breakpoint()` calls in python
+      - id: detect-private-key # Detect the presence of private keys
+      - id: end-of-file-fixer # Ensures that files end with a newline
+      - id: name-tests-test # Verify that test files are named correctly
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.2.1
+    hooks:
+      - id: prettier
+
   - repo: https://github.com/psf/black
     rev: 20.8b1
     hooks:
       - id: black
-        args: [--safe, --quiet, --line-length, "100"]
-        language_version: python3
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: "3.7.9"
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.6.4
+    hooks:
+      - id: isort
+
+  - repo: https://gitlab.com/PyCQA/flake8
+    rev: 3.8.4
     hooks:
       - id: flake8
-        args:
-          [
-            --count,
-            --select,
-            "E9,F63,F7,F82",
-            --show-source,
-            --statistics,
-            --max-complexity,
-            "10",
-            --max-line-length,
-            "100",
-          ]
-        language_version: python3
+
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.6.2
+    hooks:
+      - id: bandit
+        args: [--exclude, tests]