Merge pull request #18 from bradendubois/beta

Full release onto main for PyPI "launch"

.github/workflows/test_and_release.yml

@@ -11,19 +11,19 @@ jobs:
   test:
     strategy:
       matrix:
-        report-coverage: [ false ]
-        python-version: [ 3.8, 3.9 ]
         os:
         - ubuntu-latest
         - ubuntu-18.04
         - ubuntu-16.04
         - macos-latest
         - windows-latest
+        python-version: [ 3.8, 3.9 ]
+        report-coverage: [ false ]
 
         # Special matrix job to report coverage only once
         include:
-          - python-version: 3.9
-            os: ubuntu-latest
+          - os: ubuntu-latest
+            python-version: 3.9
             report-coverage: true
 
     runs-on: ${{ matrix.os }}
@@ -57,13 +57,57 @@ jobs:
       uses: AndreMiras/coveralls-python-action@develop
       if: ${{ matrix.report-coverage }}
 
-  release:
+  # Tag and create a new release - handled by semantic-release
+  tag:
     runs-on: ubuntu-latest
-    needs: test
+    needs: test   # Only consider creating a release if  all tests pass
+
+    # Only create a release on main / beta
     if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/beta'
     steps:
     - uses: actions/checkout@v2
     - name: Create Release
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: npx semantic-release
+
+  # Package and upload to PyPI
+  pypi:
+    runs-on: ubuntu-latest
+    needs: tag  # Need to get the latest version number, which may change based on semantic-release
+
+    # Only upload to PyPI on main
+    if: github.ref == 'refs/heads/main'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8 pytest coverage coveralls
+          pip install -r requirements.txt
+
+      - name: Get Version Number
+        uses: oprypin/find-latest-tag@v1
+        id: tag
+        with:
+          repository: ${{ github.repository }}
+          releases-only: true
+
+      - name: Build PyPI Package
+        run: |
+          python setup.py sdist bdist_wheel
+        env:
+          SEMANTIC_VERSION: ${{ steps.tag.outputs.tag }}
+
+      - name: PyPI Publish
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -10,7 +10,14 @@
 *.pyc
 
 # Log files from operating software
-src/logs/
+do-calculus/logs/
 
 # Config file is generated on run
-src/config/config.*
+*config.*
+
+*.egg*
+
+# results from building package
+build/*
+dist/*
+

MANIFEST.in

@@ -0,0 +1 @@
+include do/*

README.md

@@ -1,4 +1,4 @@
-<h1 align="center" style="border-bottom: none;">probability-code</h1>
+<h1 align="center" style="border-bottom: none;">do-calculus</h1>
 <h3 align="center">A Python implementation of the <i>do-calculus</i> of Judea Pearl et. al.</h3>
 <p align="center">
     <a href="https://github.com/bradendubois/probability-code/actions?query=workflow%3ATest+branch%3Amain">
@@ -7,17 +7,24 @@
     <a href='https://coveralls.io/github/bradendubois/probability-code?branch=main'>
         <img src='https://coveralls.io/repos/github/bradendubois/probability-code/badge.svg?branch=main' alt='Coverage Status' />
     </a>
+    <a href="https://pypi.org/project/do-calculus/">
+        <img alt="" src="https://pypip.in/v/do-calculus/badge.svg">
+    </a>
+    <a href="https://pypi.org/project/do-calculus/">
+        <img alt="" src="https://pypip.in/wheel/do-calculus/badge.svg">
+    </a>
     <a href="https://github.com/semantic-release/semantic-release">
         <img alt="semantic-release" src="https://img.shields.io/badge/%20%20%F0%9F%93%A6%F0%9F%9A%80-semantic--release-e10079.svg">
     </a>
 </p>
 
 ## Resources
 
-* **Documentation / Wiki**: https://github.com/bradendubois/probability-code/wiki
-* **Source code**: https://github.com/bradendubois/probability-code
-* **Releases**: https://github.com/bradendubois/probability-code/releases
-* **Bug reports**: https://github.com/bradendubois/probability-code/issues
+* **Documentation / Wiki**: [github.com/bradendubois/probability-code/wiki](https://github.com/bradendubois/probability-code/wiki)
+* **Source Code**: [github.com/bradendubois/probability-code](https://github.com/bradendubois/probability-code)
+* **PyPI**: [pypi.org/project/do-calculus/](https://pypi.org/project/do-calculus/)
+* **Releases**: [github.com/bradendubois/probability-code/releases](https://github.com/bradendubois/probability-code/releases)
+* **Bug reports**: [github.com/bradendubois/probability-code/issues](https://github.com/bradendubois/probability-code/issues)
 * **Contact**: [[email protected]](mailto:[email protected])
 
 See the [wiki](https://github.com/bradendubois/probability-code/wiki) to get started.

debug/README.md

@@ -0,0 +1,8 @@
+# Debug
+
+This is just a large directory of debug info I move here to root through, test files to make, etc.
+This is here so that it can be added to the Git repo and move across machines, etc. but is not included when packaged to PyPI. 
+
+- **Nothing** in this subdirectory should ever be imported/required elsewhere.
+- **Nothing** in this directory is likely to work as-is.
+

API.py → do/API.py

@@ -5,18 +5,18 @@
 from typing import Union
 from pathlib import Path
 
-from src.api.backdoor_paths import api_backdoor_paths
-from src.api.deconfounding_sets import api_deconfounding_sets
-from src.api.joint_distribution_table import api_joint_distribution_table
-from src.api.probability_query import api_probability_query
-
-from src.probability.structures.BackdoorController import BackdoorController
-from src.probability.structures.CausalGraph import CausalGraph
-from src.probability.structures.ConditionalProbabilityTable import ConditionalProbabilityTable
-from src.probability.structures.VariableStructures import Variable
-
-from src.util.ModelLoader import parse_model
-from src.util.OutputLogger import OutputLogger
+from .api.backdoor_paths import api_backdoor_paths
+from .api.deconfounding_sets import api_deconfounding_sets
+from .api.joint_distribution_table import api_joint_distribution_table
+from .api.probability_query import api_probability_query
+
+from .probability.structures.BackdoorController import BackdoorController
+from .probability.structures.CausalGraph import CausalGraph
+from .probability.structures.ConditionalProbabilityTable import ConditionalProbabilityTable
+from .probability.structures.VariableStructures import Variable
+
+from .util.ModelLoader import parse_model
+from .util.OutputLogger import OutputLogger
 
 
 class Do:

do/__init__.py

@@ -0,0 +1,7 @@
+__all__ = [
+    "api",
+    "config",
+    "probability",
+    "util",
+    "API",
+]

src/REPL.py → do/__main__.py

@@ -1,19 +1,18 @@
 from yaml import safe_load as load
-from os import path, listdir
 from pathlib import Path
 
-from src.api.backdoor_paths import api_backdoor_paths_parse
-from src.api.deconfounding_sets import api_deconfounding_sets_parse
-from src.api.probability_query import api_probability_query_parse
+from .api.backdoor_paths import api_backdoor_paths_parse
+from .api.deconfounding_sets import api_deconfounding_sets_parse
+from .api.probability_query import api_probability_query_parse
 
-from API import Do
+from .API import Do
 
 
 # TODO - Change graph_location to allow a specific graph to be given and loaded, or specify a user directory without
 #   there being path issues depending on the working directory
 
 
-def run_repl(graph_location=Path(".", "src", "graphs", "full")):
+def main(graph_location=Path(".", "src", "graphs", "full")):
     """
     Run an interactive IO prompt allowing full use of the causality software.
     @param graph_location: A string of the path from the working directory to a directory of graphs

do/api/__init__.py

@@ -0,0 +1,6 @@
+__all__ = [
+    "backdoor_paths",
+    "deconfounding_sets",
+    "joint_distribution_table",
+    "probability_query"
+]

src/api/backdoor_paths.py → do/api/backdoor_paths.py

@@ -1,6 +1,6 @@
 from itertools import product
 
-from src.probability.structures.BackdoorController import BackdoorController
+from ..probability.structures.BackdoorController import BackdoorController
 
 
 def api_backdoor_paths_parse(query: str) -> (set, set):

src/api/deconfounding_sets.py → do/api/deconfounding_sets.py

@@ -1,4 +1,4 @@
-from src.probability.structures.BackdoorController import BackdoorController
+from ..probability.structures.BackdoorController import BackdoorController
 
 
 def api_deconfounding_sets_parse(query: str) -> (set, set):

src/api/joint_distribution_table.py → do/api/joint_distribution_table.py

@@ -1,7 +1,8 @@
 from itertools import product
-from src.probability.structures.CausalGraph import CausalGraph
-from src.probability.structures.ConditionalProbabilityTable import ConditionalProbabilityTable
-from src.probability.structures.VariableStructures import Outcome, Variable
+
+from ..probability.structures.CausalGraph import CausalGraph
+from ..probability.structures.ConditionalProbabilityTable import ConditionalProbabilityTable
+from ..probability.structures.VariableStructures import Outcome, Variable
 
 
 def api_joint_distribution_table(cg: CausalGraph) -> ConditionalProbabilityTable:

src/api/probability_query.py → do/api/probability_query.py

@@ -1,5 +1,5 @@
-from src.probability.structures.CausalGraph import CausalGraph
-from src.probability.structures.VariableStructures import parse_outcomes_and_interventions
+from ..probability.structures.CausalGraph import CausalGraph
+from ..probability.structures.VariableStructures import parse_outcomes_and_interventions
 
 
 def api_probability_query_parse(query: str) -> (tuple, tuple):

do/config/__init__.py

@@ -0,0 +1,5 @@
+__all__ = [
+    "config_manager",
+    "primary_configuration",
+    "settings"
+]

do/config/config.yml

@@ -0,0 +1,5 @@
+cache_computation_results: true
+minimize_backdoor_sets: true
+output_levels_of_precision: 5
+regression_levels_of_precision: 5
+topological_sort_variables: true

src/config/config_manager.py → do/config/config_manager.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 from yaml import safe_load as load, dump
 
-from src.config.primary_configuration import *
+from ..config.primary_configuration import *
 
-path = Path(".", "src", "config", "config.yml")
+path = Path(".", "config.yml")
 
 
 def create_default():

src/config/generate_config_docs.py → do/config/generate_config_docs.py

@@ -4,7 +4,7 @@
 
 from pathlib import Path
 
-from primary_configuration import *
+from .primary_configuration import *
 
 documentation_file = Path(".", "doc", "Configuration.md")
 

src/config/settings.py → do/config/settings.py

@@ -1,4 +1,4 @@
-from src.config.config_manager import settings_yml
+from .config_manager import settings_yml
 
 
 class Settings:

do/probability/__init__.py

@@ -0,0 +1,3 @@
+__all__ = [
+    "structures"
+]

src/probability/structures/BackdoorController.py → do/probability/structures/BackdoorController.py

@@ -9,10 +9,11 @@
 
 from itertools import product
 
-from src.config.settings import Settings
-from src.probability.structures.Graph import Graph
-from src.util.helpers import minimal_sets
-from src.util.helpers import power_set
+from .Graph import Graph
+
+from ...config.settings import Settings
+from ...util.helpers import minimal_sets
+from ...util.helpers import power_set
 
 
 class BackdoorController:

src/probability/structures/CausalGraph.py → do/probability/structures/CausalGraph.py

@@ -9,15 +9,14 @@
 
 from itertools import product
 
-from src.config.settings import Settings
-
-from src.probability.structures.BackdoorController import BackdoorController
-from src.probability.structures.Graph import Graph
-from src.probability.structures.Probability_Engine import ProbabilityEngine
-from src.probability.structures.VariableStructures import Outcome, Intervention
-
-from src.util.OutputLogger import OutputLogger
-from src.util.helpers import p_str
+from .BackdoorController import BackdoorController
+from .Graph import Graph
+from .Probability_Engine import ProbabilityEngine
+from .VariableStructures import Outcome, Intervention
+
+from ...config.settings import Settings
+from ...util.OutputLogger import OutputLogger
+from ...util.helpers import p_str
 
 
 class CausalGraph:

src/probability/structures/ConditionalProbabilityTable.py → do/probability/structures/ConditionalProbabilityTable.py

@@ -1,4 +1,4 @@
-#                                                       #
+#########################################################
 #   Causal Graph                                        #
 #                                                       #
 #   Author: Braden Dubois ([email protected])      #
@@ -9,9 +9,10 @@
 from numpy import empty
 from math import floor, ceil
 
-from src.config.settings import Settings
-from src.probability.structures.VariableStructures import Variable, Outcome, Intervention
-from src.util.ProbabilityExceptions import MissingTableRow
+from .VariableStructures import Variable, Outcome, Intervention
+
+from ...config.settings import Settings
+from ...util.ProbabilityExceptions import MissingTableRow
 
 
 class ConditionalProbabilityTable:

src/probability/structures/Graph.py → do/probability/structures/Graph.py

@@ -13,7 +13,7 @@
 
 from typing import Union
 
-from src.probability.structures.VariableStructures import *
+from .VariableStructures import Variable, Outcome, Intervention
 
 # These functions should work with any sort of Variable type, or the name itself
 CG_Types = Union[str, Variable, Outcome, Intervention]

src/probability/structures/Probability_Engine.py → do/probability/structures/Probability_Engine.py

@@ -9,14 +9,13 @@
 
 from itertools import product
 
-from src.config.settings import Settings
+from .Graph import Graph
+from .VariableStructures import Outcome, Intervention
 
-from src.probability.structures.Graph import Graph
-from src.probability.structures.VariableStructures import Outcome, Intervention
-
-from src.util.OutputLogger import OutputLogger
-from src.util.helpers import p_str
-from src.util.ProbabilityExceptions import ProbabilityException, ProbabilityIndeterminableException
+from ...config.settings import Settings
+from ...util.OutputLogger import OutputLogger
+from ...util.helpers import p_str
+from ...util.ProbabilityExceptions import ProbabilityException, ProbabilityIndeterminableException
 
 
 class ProbabilityEngine:

do/probability/structures/__init__.py

@@ -0,0 +1,8 @@
+__all__ = [
+    "BackdoorController",
+    "CausalGraph",
+    "ConditionalProbabilityTable",
+    "Graph",
+    "Probability_Engine",
+    "VariableStructures"
+]