ODME (#504)

* Squashed ODME

* .

* rename

* xample notebook

* .

* .

* Rename

* Select link problem script no longer needed (Issue #493 resolved)

* Rename & add saving stub

* Created saving test

* Removed whitespace

* Rename to avoid name conflict

* Fixed _prepare_execute

* __id__ changed to _id in TrafficClass

* Removed statistics gathering from main class (use the results class for this now)

* Reworked results to have dataframe for links and for iterations

* Fixed bugs in last commit

* Fixed bug in test where wrong name used for assignment results

* Deleted redundant script (this is now a test)

* Updated results to allow for empty dataframe return if no execution

* Updated final script - results still not fully working and saving requires more testing.

* Fixed bug where results were being suppressed by incorrect if/else order

* Changed comment

* updated comment

* Finished clean up of ODME main class, 3 TODO's remaining until this class is completed fully.

* Same as last commit (forgot to do extra part of commit)

* made pytlint happier

* ODMEResults class cleaned up - no TODO's remaining here.

* Cleaned up ScalingFactors - 6 todo's 5 of which are referencing.

* Added in-text citations to Spiess

* make pylint happy

* pushing stuff

* add support for json report on matrices

* run black linter

* Removed Todo

* Tidied up example usage doc

* Scripts Finalised

* Dealt with multi-class objective function pce

* Removed comment

* .

* Finished all plot generation and scripts

* .

* .

* .

* Rename file

* Updated example doc & deleted scripts

* Added matrix_estimation.rst file

* Partially updated .rst file

* more writing

* 3 sections unfinished

* Updated example script

* .

* Edited overview

* Finished Execution block

* Results block finished

* Completed

* Update docs/source/examples/full_workflows/plot_matrix_estimation.py

---------

Co-authored-by: Jamie Cook <[email protected]>
Co-authored-by: mitsudz <[email protected]>

.devcontainer/Dockerfile

@@ -0,0 +1,21 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3/.devcontainer/base.Dockerfile
+
+# [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster
+ARG VARIANT="3.10-bullseye"
+FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT}
+
+# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# COPY requirements.txt /tmp/pip-tmp/
+# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+#    && rm -rf /tmp/pip-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

@@ -0,0 +1,58 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3
+{
+	"name": "Python 3",
+	"build": {
+		"dockerfile": "Dockerfile",
+		"context": "..",
+		"args": { 
+			// Update 'VARIANT' to pick a Python version: 3, 3.10, 3.9, 3.8, 3.7, 3.6
+			// Append -bullseye or -buster to pin to an OS version.
+			// Use -bullseye variants on local on arm64/Apple Silicon.
+			"VARIANT": "3.10-bullseye",
+			// Options
+			"NODE_VERSION": "none"
+		}
+	},
+
+	// Configure tool-specific properties.
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+			// Set *default* container specific settings.json values on container create.
+			"settings": { 
+				"python.defaultInterpreterPath": "/usr/local/bin/python",
+				"python.linting.enabled": true,
+				"python.linting.pylintEnabled": true,
+				"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+				"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+				"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+				"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+				"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
+				"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+				"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+				"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+				"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+			},
+
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-python.python",
+				"ms-python.vscode-pylance"
+			]
+		}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "pip3 install --user -r requirements.txt",
+
+	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "vscode",
+	"features": {
+		"git": "latest",
+		"jupyterlab": "latest"
+	}
+}

.gitignore

@@ -96,3 +96,12 @@ build/
 coverage.xml
 
 #### End snippet
+.DS_Store
+
+# Images
+*.png
+*.csv
+
+# Aequilibrae Procedure Log
+*.log
+*.qgz

aequilibrae/__init__.py

@@ -28,6 +28,7 @@
 from aequilibrae.paths.assignment_paths import AssignmentPaths
 from aequilibrae.project import Project
 from aequilibrae.paths.results import AssignmentResults, SkimResults, PathResults
+from aequilibrae.paths.odme import ODME
 
 from aequilibrae import paths
 

aequilibrae/paths/__init__.py

@@ -9,6 +9,8 @@
 from aequilibrae.paths.vdf import VDF
 from aequilibrae.paths.graph import Graph, TransitGraph
 
+from aequilibrae.paths.odme import ODME
+
 from aequilibrae import global_logger