From a89a08a81ba7813a892ca8613fdfc5db0577208c Mon Sep 17 00:00:00 2001 From: BambooUser-IDM Date: Fri, 8 Aug 2025 21:42:19 +0000 Subject: [PATCH 1/2] =?UTF-8?q?Bump=20version:=201.0.1=20=E2=86=92=201.0.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- emodpy_workflow/__init__.py | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 81351c0..b63c933 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.0.1 +current_version = 1.0.2 commit = False tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)((?P[\+a-z]+)\.(?P\d+))? diff --git a/emodpy_workflow/__init__.py b/emodpy_workflow/__init__.py index 5c4105c..7863915 100644 --- a/emodpy_workflow/__init__.py +++ b/emodpy_workflow/__init__.py @@ -1 +1 @@ -__version__ = "1.0.1" +__version__ = "1.0.2" diff --git a/pyproject.toml b/pyproject.toml index 0279ead..e080c32 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" [project] name = "emodpy-workflow" -version = "1.0.1" +version = "1.0.2" description = "IDM's emodpy modeling workflow scripts and supporting libraries" readme = "README.md" requires-python = ">=3.9" From 542e3c379258c41f7d194278cf385d494805a3de Mon Sep 17 00:00:00 2001 From: Jen Schripsema Date: Tue, 25 Nov 2025 12:49:46 -0700 Subject: [PATCH 2/2] added GTM container, standardized capitalization, removed unecessary JS file --- docs/customization/javascripts/mathjax.js | 19 ----------------- .../integrations/analytics/custom.html | 21 +++++++++++++++++++ docs/how_to/how_to_ingest_form.md | 2 +- docs/reference/age_bin_format.md | 2 +- docs/reference/ingest_form.md | 2 +- docs/reference/sweeps.md | 2 +- docs/reference/virtual_environments.md | 2 +- docs/tutorials/create_project.md | 6 +++--- docs/tutorials/get_started.md | 2 +- docs/tutorials/modify_configuration.md | 2 +- docs/tutorials/modify_reports.md | 2 +- docs/tutorials/run_calibration.md | 2 +- docs/tutorials/run_emod.md | 6 +++--- docs/tutorials/setup.md | 2 +- docs/tutorials/sweep_parameter.md | 2 +- mkdocs.yml | 7 +++---- 16 files changed, 41 insertions(+), 40 deletions(-) delete mode 100644 docs/customization/javascripts/mathjax.js create mode 100644 docs/customization/overrides/partials/integrations/analytics/custom.html diff --git a/docs/customization/javascripts/mathjax.js b/docs/customization/javascripts/mathjax.js deleted file mode 100644 index f0d0ad5..0000000 --- a/docs/customization/javascripts/mathjax.js +++ /dev/null @@ -1,19 +0,0 @@ -window.MathJax = { - tex: { - inlineMath: [["\\(", "\\)"]], - displayMath: [["\\[", "\\]"]], - processEscapes: true, - processEnvironments: true - }, - options: { - ignoreHtmlClass: ".*|", - processHtmlClass: "arithmatex" - } -}; - -document$.subscribe(() => { - MathJax.startup.output.clearCache() - MathJax.typesetClear() - MathJax.texReset() - MathJax.typesetPromise() -}) \ No newline at end of file diff --git a/docs/customization/overrides/partials/integrations/analytics/custom.html b/docs/customization/overrides/partials/integrations/analytics/custom.html new file mode 100644 index 0000000..5ecb4bd --- /dev/null +++ b/docs/customization/overrides/partials/integrations/analytics/custom.html @@ -0,0 +1,21 @@ +{# page partial for GTM analytics code, extends "!page.html" +#} + +{% block extrahead %} + + + + + + + + + + + +{% endblock %} diff --git a/docs/how_to/how_to_ingest_form.md b/docs/how_to/how_to_ingest_form.md index 5cf096f..8f694bc 100644 --- a/docs/how_to/how_to_ingest_form.md +++ b/docs/how_to/how_to_ingest_form.md @@ -1,4 +1,4 @@ -# Ingest Form +# Ingest form The [filling an ingest form reference](../reference/ingest_form.md) covers the context in which the macros noted in this how-to are used. diff --git a/docs/reference/age_bin_format.md b/docs/reference/age_bin_format.md index 5413a7f..d1c5531 100644 --- a/docs/reference/age_bin_format.md +++ b/docs/reference/age_bin_format.md @@ -1,4 +1,4 @@ -# Ingest Form Age Bin Format +# Ingest form age bin format The ingest form uses a particular format for age bins. These age bins are used on multiple sheets: **Site**, **Analyzers**, and **observational data** sheets. diff --git a/docs/reference/ingest_form.md b/docs/reference/ingest_form.md index f4c5582..cc1cbf2 100644 --- a/docs/reference/ingest_form.md +++ b/docs/reference/ingest_form.md @@ -1,4 +1,4 @@ -# Ingest Form +# Ingest form An ingest form is a multi-sheet Excel spreadsheet that organizes reference data and sets analysis controls for the `calibrate` command. It controls the non-iterative aspects of a calibration process, while the `calibrate` diff --git a/docs/reference/sweeps.md b/docs/reference/sweeps.md index 2e07ce7..9cbf97a 100644 --- a/docs/reference/sweeps.md +++ b/docs/reference/sweeps.md @@ -1,4 +1,4 @@ -# **Sweep files** +# Sweep files A sweep file is a Python file that specifies sets of hyperparameter overrides, often referred to as "scenarios". Scenarios address specific scientific questions, diff --git a/docs/reference/virtual_environments.md b/docs/reference/virtual_environments.md index ef94492..bd8f9da 100644 --- a/docs/reference/virtual_environments.md +++ b/docs/reference/virtual_environments.md @@ -1,4 +1,4 @@ -# Virtual Environments +# Virtual environments ## Why use virtual environments diff --git a/docs/tutorials/create_project.md b/docs/tutorials/create_project.md index 7d9a261..42474e6 100644 --- a/docs/tutorials/create_project.md +++ b/docs/tutorials/create_project.md @@ -1,4 +1,4 @@ -# Create Project +# Create a project ## Objective @@ -318,8 +318,8 @@ country model. See the other tutorials on modifying the configuration: - - [Modify Configuration](modify_configuration.md) - - [Modify Campaign](modify_campaign.md) + - [Modify configuration](modify_configuration.md) + - [Modify campaign](modify_campaign_1_minimal_campaign.md) ## Next up: Running your baseline frame diff --git a/docs/tutorials/get_started.md b/docs/tutorials/get_started.md index 3fa6285..bfa6599 100644 --- a/docs/tutorials/get_started.md +++ b/docs/tutorials/get_started.md @@ -1,4 +1,4 @@ -# Get Started with EMOD-HIV and emodpy-workflow +# Get started with EMOD-HIV and emodpy-workflow ## Assumptions diff --git a/docs/tutorials/modify_configuration.md b/docs/tutorials/modify_configuration.md index b00c302..4c4f0f7 100644 --- a/docs/tutorials/modify_configuration.md +++ b/docs/tutorials/modify_configuration.md @@ -1,4 +1,4 @@ -# Modify Configuration Parameters +# Modify configuration parameters Configuration parameters are simulation-wide parameters that affect how EMOD runs at a fundamental level. These include parameters related, but not limited to: diff --git a/docs/tutorials/modify_reports.md b/docs/tutorials/modify_reports.md index bdde23d..a86035f 100644 --- a/docs/tutorials/modify_reports.md +++ b/docs/tutorials/modify_reports.md @@ -1,4 +1,4 @@ -# Modify Reports +# Modify reports Reports are output (files) generated by EMOD. There are multiple built-in EMOD reports that are configured by Python code as well as the ability to create custom reports for a project. diff --git a/docs/tutorials/run_calibration.md b/docs/tutorials/run_calibration.md index 98a4cf2..2a7dbc6 100644 --- a/docs/tutorials/run_calibration.md +++ b/docs/tutorials/run_calibration.md @@ -1,4 +1,4 @@ -# Run Calibration +# Run calibration ## What is calibration? diff --git a/docs/tutorials/run_emod.md b/docs/tutorials/run_emod.md index 3731629..3ab2d71 100644 --- a/docs/tutorials/run_emod.md +++ b/docs/tutorials/run_emod.md @@ -792,8 +792,8 @@ in the simulation. Now that you have run EMOD once, investigate the other tutorials where you can modify the simulation and run the model. -- [Modify Reports](modify_reports.md) -- [Modify Configuration](modify_configuration.md) -- [Modify Campaign](modify_campaign.md) +- [Modify reports](modify_reports.md) +- [Modify configuration](modify_configuration.md) +- [Modify campaign](modify_campaign_1_minimal_campaign.md) diff --git a/docs/tutorials/setup.md b/docs/tutorials/setup.md index 3bfa053..61f655a 100644 --- a/docs/tutorials/setup.md +++ b/docs/tutorials/setup.md @@ -1,4 +1,4 @@ -# Install and Set Up +# Install and set up ## Choose to run the tutorials locally or use [GitHub Codespaces](https://docs.github.com/en/codespaces/about-codespaces/what-are-codespaces). diff --git a/docs/tutorials/sweep_parameter.md b/docs/tutorials/sweep_parameter.md index a575ffb..07274ac 100644 --- a/docs/tutorials/sweep_parameter.md +++ b/docs/tutorials/sweep_parameter.md @@ -1,4 +1,4 @@ -# Create Scenarios and Do Sweeps +# Create scenarios and do sweeps This tutorial utilizes ParameterizedCalls. The tutorial covering them is located [here](use_parameterized_calls.md) and should be completed first. diff --git a/mkdocs.yml b/mkdocs.yml index 2c36999..eee3c74 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -111,7 +111,7 @@ plugins: - mkdocs-jupyter: # enables Jupyter notebooks to be rendered execute: true allow_errors: false # set to true to continue executing cells even if one fails - include-source: true + include_source: true copyright: Copyright © 2025 Gates Foundation. All rights reserved. @@ -135,9 +135,8 @@ extra: link: https://linkedin.com/company/institute-disease-modeling analytics: - provider: google - property: G-SVDSQH04EM - tracking_id: # no tracking until we can implement OneTrust cookie consent + provider: custom + property: GTM-NK4K647 feedback: title: Was this page helpful? ratings: