pylantir 0.1.1__tar.gz → 0.1.2__tar.gz

{pylantir-0.1.1 → pylantir-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylantir
-Version: 0.1.1
+Version: 0.1.2
 Summary: Python - DICOM Modality WorkList
 Author-email: Milton Camacho <miltoncamachoicc@gmail.com>
 Requires-Python: >=3.11.1

{pylantir-0.1.1 → pylantir-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name =  "pylantir"
-version = "0.1.1"
+version = "0.1.2"
 authors = [
     {name = "Milton Camacho", email = "miltoncamachoicc@gmail.com"},
 ]

{pylantir-0.1.1 → pylantir-0.1.2}/src/pylantir/__init__.py

@@ -5,4 +5,4 @@
 """Python Package Template"""
 from __future__ import annotations
 
-__version__ = "0.0.2-rc76-post1"
+__version__ = "0.0.2"

{pylantir-0.1.1 → pylantir-0.1.2}/src/pylantir/redcap_to_db.py

@@ -241,7 +241,7 @@ def sync_redcap_to_db_repeatedly(
 
     # last_sync_date = datetime.now().date()
     last_sync_date = datetime.now().date() - timedelta(days=1)
-    interval_sync = interval + 600 # add 10 minutes to the interval to overlap with the previous sync and avoid missing data
+    interval_sync = interval + 300 # add 5 minutes to the interval to overlap with the previous sync and avoid missing data
 
     while not STOP_EVENT.is_set():
         # === 1) BASELINE: set defaults for flags and wait-time each iteration ===
@@ -271,7 +271,7 @@ def sync_redcap_to_db_repeatedly(
                 logging.info(f"Using extended interval: {extended_interval}, {interval} seconds until next sync.")
             else:
                 # Either not first run, or last_sync_date is None (this is first-ever run)
-                logging.info("Using default interval {interval} seconds.")
+                logging.info(f"Using default interval {interval} seconds.")
 
             # --- CALL THE SYNC FUNCTION INSIDE A TRY/EXCEPT ---
             logging.debug(f"Syncing REDCap to DB for site {site_id} at {now_time}.")

pylantir-0.1.1/.devcontainer/Dockerfile

@@ -1,12 +0,0 @@
-FROM mcr.microsoft.com/devcontainers/python:3
-
-RUN python -m pip install --upgrade pip \
-    && python -m pip install 'flit>=3.8.0'
-
-ENV FLIT_ROOT_INSTALL=1
-
-COPY pyproject.toml .
-RUN touch README.md \
-    && mkdir -p src/python_package \
-    && python -m flit install --only-deps --deps develop \
-    && rm -r pyproject.toml README.md src

pylantir-0.1.1/.devcontainer/devcontainer.json

@@ -1,44 +0,0 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containers/tree/v0.222.0/containers/python-3-miniconda
-{
-	"name": "Python Environment",
-	"build": {
-		"dockerfile": "Dockerfile",
-		"context": ".."
-	},
-	"customizations": {
-		"vscode": {
-			"extensions": [
-				"editorconfig.editorconfig",
-				"github.vscode-pull-request-github",
-				"ms-azuretools.vscode-docker",
-				"ms-python.python",
-				"ms-python.vscode-pylance",
-				"ms-python.pylint",
-				"ms-python.isort",
-				"ms-python.flake8",
-				"ms-python.black-formatter",
-				"ms-vsliveshare.vsliveshare",
-				"ryanluker.vscode-coverage-gutters",
-				"bungcip.better-toml",
-				"GitHub.copilot"
-			],
-			"settings": {
-				"python.defaultInterpreterPath": "/usr/local/bin/python",
-				"black-formatter.path": [
-					"/usr/local/py-utils/bin/black"
-				],
-				"pylint.path": [
-					"/usr/local/py-utils/bin/pylint"
-				],
-				"flake8.path": [
-					"/usr/local/py-utils/bin/flake8"
-				],
-				"isort.path": [
-					"/usr/local/py-utils/bin/isort"
-				]
-			}
-		}
-	},
-	"onCreateCommand": "pre-commit install-hooks"
-}

pylantir-0.1.1/.github/dependabot.yml

@@ -1,22 +0,0 @@
-version: 2
-updates:
-- package-ecosystem: pip
-  directory: "/"
-  schedule:
-    interval: daily
-    time: "13:00"
-  open-pull-requests-limit: 10
-  reviewers:
-  - dciborow
-  allow:
-  - dependency-type: direct
-  - dependency-type: indirect
-  commit-message:
-    prefix: "fix: "
-- package-ecosystem: "github-actions"
-  directory: "/"
-  schedule:
-    interval: daily
-    time: "13:00"
-  commit-message:
-    prefix: "fix: "

pylantir-0.1.1/.github/template-sync.yml

@@ -1,21 +0,0 @@
-files:
-  - ".gitignore"  # include
-  - ".github"
-  - ".vscode"
-  - "tests/conftest.py"
-  - ".flake8"
-  - ".pre-commit-config.yml"
-  - ".pypirc"
-  - "docs"
-  - "src/README.md"
-  - "CODE_OF_CONDUCT.md"
-  - "LICENSE"
-  - "README.md"
-  - "SECURITY.md"
-  - "SUPPORT.md"
-  - "pyproject.toml"
-
-  - "!.github/workflows/template-sync.yml"
-  - "!.github/template-sync.yml"
-  - "!src/python_project"
-  - "!tests/test_methods.py"

pylantir-0.1.1/.github/workflows/CI.yml

@@ -1,21 +0,0 @@
-name: Python CI
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-  release:
-    types: [created]    
-  workflow_dispatch:
-
-jobs:
-  validation:
-    uses: microsoft/action-python/.github/workflows/validation.yml@0.6.4
-    with:
-      workdir: '.'
-
-  publish:
-    uses: microsoft/action-python/.github/workflows/publish.yml@0.6.4
-    secrets:
-      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      TEST_PYPI_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD  }}

pylantir-0.1.1/.github/workflows/publish.yml

@@ -1,33 +0,0 @@
-name: Publish Python Package
-
-on:
-  push:
-    tags:
-      - "v*"  # Only run on version tags like v1.2.3
-
-jobs:
-  build-and-publish:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-
-      - name: Install build tools
-        run: |
-          python -m pip install --upgrade pip
-          pip install build twine
-
-      - name: Build package
-        run: python -m build
-
-      - name: Publish to PyPI
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: twine upload dist/*

pylantir-0.1.1/.github/workflows/schedule-update-actions.yml

@@ -1,25 +0,0 @@
-name: GitHub Actions Version Updater
-
-# Controls when the action will run.
-on:
-  workflow_dispatch:
-  schedule:
-    # Automatically run on every Sunday
-    - cron:  '0 0 * * 0'
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3.5.2
-        with:
-          # [Required] Access token with `workflow` scope.
-          token: ${{ secrets.PAT }}
-
-      - name: Run GitHub Actions Version Updater
-        uses: saadmk11/github-actions-version-updater@v0.7.4
-        with:
-          # [Required] Access token with `workflow` scope.
-          token: ${{ secrets.PAT }}
-          pull_request_title: "ci: Update GitHub Actions to Latest Version"

pylantir-0.1.1/.github/workflows/semantic-pr-check.yml

@@ -1,17 +0,0 @@
-name: "Semantic PR Check"
-
-on:
-  pull_request_target:
-    types:
-      - opened
-      - edited
-      - synchronize
-
-jobs:
-  main:
-    name: Validate PR title
-    runs-on: ubuntu-latest
-    steps:
-      - uses: amannn/action-semantic-pull-request@v5.2.0
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

pylantir-0.1.1/.github/workflows/sphinx.yml

@@ -1,18 +0,0 @@
-name: Deploy Sphinx documentation to Pages
-
-on:
-  push:
-    branches: [main] # branch to trigger deployment
-
-jobs:
-  pages:
-    runs-on: ubuntu-20.04
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    permissions:
-      pages: write
-      id-token: write
-    steps:
-    - id: deployment
-      uses: sphinx-notes/pages@v3

pylantir-0.1.1/.github/workflows/template-sync.yml

@@ -1,12 +0,0 @@
-name: Template Sync
-on:
-  workflow_dispatch:
-jobs:
-  sync:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3.5.2 # important!
-      - uses: euphoricsystems/action-sync-template-repository@v2.5.1
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          dry-run: true

pylantir-0.1.1/.gitignore

@@ -1,129 +0,0 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/

pylantir-0.1.1/.pre-commit-config.yaml

@@ -1,60 +0,0 @@
-ci:
-  autoupdate_commit_msg: "chore: update pre-commit hooks"
-  autofix_commit_msg: "style: pre-commit fixes"
-
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
-    hooks:
-      - id: check-added-large-files
-      - id: check-case-conflict
-      - id: check-merge-conflict
-      - id: check-symlinks
-      - id: check-yaml
-      - id: debug-statements
-      - id: end-of-file-fixer
-      - id: mixed-line-ending
-      - id: requirements-txt-fixer
-      - id: trailing-whitespace
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-        args: ["-a", "from __future__ import annotations"]
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.0
-    hooks:
-      - id: pyupgrade
-        args: [--py37-plus]
-
-  - repo: https://github.com/hadialqattan/pycln
-    rev: v1.2.5
-    hooks:
-      - id: pycln
-        args: [--config=pyproject.toml]
-        stages: [manual]
-
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
-    hooks:
-      - id: codespell
-
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
-    hooks:
-      - id: python-check-blanket-noqa
-      - id: python-check-blanket-type-ignore
-      - id: python-no-log-warn
-      - id: python-no-eval
-      - id: python-use-type-annotations
-      - id: rst-backticks
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
-
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
-    hooks:
-      - id: check-manifest
-        stages: [manual]

pylantir-0.1.1/.pypirc

@@ -1,10 +0,0 @@
-[distutils]
-index-servers =
-    pypi
-    testpypi
-
-[pypi]
-repository = https://upload.pypi.org/legacy/
-
-[testpypi]
-repository = https://test.pypi.org/legacy/

pylantir-0.1.1/.vscode/launch.json

@@ -1,19 +0,0 @@
-{
-    "version": "0.1.0",
-    "configurations": [
-        {
-            "name": "Python: Debug Tests",
-            "type": "python",
-            "request": "launch",
-            "program": "${file}",
-            "purpose": [
-                "debug-test"
-            ],
-            "console": "integratedTerminal",
-            "justMyCode": false,
-            "env": {
-                "PYTEST_ADDOPTS": "--no-cov -n0 --dist no"
-            }
-        }
-    ]
-}

pylantir-0.1.1/.vscode/settings.json

@@ -1,29 +0,0 @@
-{
-    "editor.formatOnSave": true,
-    "editor.formatOnPaste": true,
-    "files.trimTrailingWhitespace": true,
-    "files.autoSave": "onFocusChange",
-    "git.autofetch": true,
-    "[jsonc]": {
-        "editor.defaultFormatter": "vscode.json-language-features"
-    },
-    "[python]": {
-        "editor.defaultFormatter": "ms-python.black-formatter"
-    },
-    "python.defaultInterpreterPath": "/usr/local/bin/python",
-    "python.formatting.provider": "black",
-    "python.testing.unittestEnabled": false,
-    "python.testing.pytestEnabled": true,
-    "pylint.args": [
-        "--rcfile=pyproject.toml"
-    ],
-    "black-formatter.args": [
-        "--config=pyproject.toml"
-    ],
-    "flake8.args": [
-        "--toml-config=pyproject.toml"
-    ],
-    "isort.args": [
-        "--settings-path=pyproject.toml"
-    ]
-}

pylantir-0.1.1/CODE_OF_CONDUCT.md

@@ -1,9 +0,0 @@
-# Microsoft Open Source Code of Conduct
-
-This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
-
-Resources:
-
-- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
-- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
-- Contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with questions or concerns

pylantir-0.1.1/SECURITY.md

@@ -1,41 +0,0 @@
-<!-- BEGIN MICROSOFT SECURITY.MD V0.0.5 BLOCK -->
-
-## Security
-
-Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/Microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet), [Xamarin](https://github.com/xamarin), and [our GitHub organizations](https://opensource.microsoft.com/).
-
-If you believe you have found a security vulnerability in any Microsoft-owned repository that meets [Microsoft's definition of a security vulnerability](https://docs.microsoft.com/en-us/previous-versions/tn-archive/cc751383(v=technet.10)), please report it to us as described below.
-
-## Reporting Security Issues
-
-**Please do not report security vulnerabilities through public GitHub issues.**
-
-Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://msrc.microsoft.com/create-report).
-
-If you prefer to submit without logging in, send email to [secure@microsoft.com](mailto:secure@microsoft.com).  If possible, encrypt your message with our PGP key; please download it from the [Microsoft Security Response Center PGP Key page](https://www.microsoft.com/en-us/msrc/pgp-key-msrc).
-
-You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://www.microsoft.com/msrc).
-
-Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
-
-  * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
-  * Full paths of source file(s) related to the manifestation of the issue
-  * The location of the affected source code (tag/branch/commit or direct URL)
-  * Any special configuration required to reproduce the issue
-  * Step-by-step instructions to reproduce the issue
-  * Proof-of-concept or exploit code (if possible)
-  * Impact of the issue, including how an attacker might exploit the issue
-
-This information will help us triage your report more quickly.
-
-If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://microsoft.com/msrc/bounty) page for more details about our active programs.
-
-## Preferred Languages
-
-We prefer all communications to be in English.
-
-## Policy
-
-Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://www.microsoft.com/en-us/msrc/cvd).
-
-<!-- END MICROSOFT SECURITY.MD BLOCK -->

pylantir-0.1.1/SUPPORT.md

@@ -1,25 +0,0 @@
-# TODO: The maintainer of this repo has not yet edited this file
-
-**REPO OWNER**: Do you want Customer Service & Support (CSS) support for this product/project?
-
-- **No CSS support:** Fill out this template with information about how to file issues and get help.
-- **Yes CSS support:** Fill out an intake form at [aka.ms/spot](https://aka.ms/spot). CSS will work with/help you to determine next steps. More details also available at [aka.ms/onboardsupport](https://aka.ms/onboardsupport).
-- **Not sure?** Fill out a SPOT intake as though the answer were "Yes". CSS will help you decide.
-
-*Then remove this first heading from this SUPPORT.MD file before publishing your repo.*
-
-# Support
-
-## How to file issues and get help
-
-This project uses GitHub Issues to track bugs and feature requests. Please search the existing
-issues before filing new issues to avoid duplicates.  For new issues, file your bug or
-feature request as a new Issue.
-
-For help and questions about using this project, please **REPO MAINTAINER: INSERT INSTRUCTIONS HERE
-FOR HOW TO ENGAGE REPO OWNERS OR COMMUNITY FOR HELP. COULD BE A STACK OVERFLOW TAG OR OTHER
-CHANNEL. WHERE WILL YOU HELP PEOPLE?**.
-
-## Microsoft Support Policy
-
-Support for this **PROJECT or PRODUCT** is limited to the resources listed above.

pylantir-0.1.1/docs/Makefile

@@ -1,20 +0,0 @@
-# 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     = .
-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)