Release cycle, ? 2025

build/local_install_or_update

@@ -0,0 +1,58 @@
+#!/usr/bin/env bash
+
+# Generic setup
+set -e
+
+# Ensure we have a $FLEPI_PATH
+if [ -z "${FLEPI_PATH}" ]; then
+    export FLEPI_PATH=$(realpath "$(pwd)")
+    if [ "$(basename "$FLEPI_PATH")" != "flepiMoP" ]; then 
+    echo "Could not find flepiMoP repository in your current directory."
+    exit 1
+    fi
+    echo "Using '$FLEPI_PATH' for \$FLEPI_PATH."
+fi
+
+# Test that flepiMoP is located there, exit if not
+if [ ! -d "$FLEPI_PATH" ]; then
+    echo "Could not find flepiMoP repository in your current directory. Please make sure you have correctly cloned flepiMoP in this directory."
+    exit 1
+fi
+
+# Ensure that conda environment is named flepimop-env
+if [ -z "${FLEPI_CONDA}" ]; then
+    export FLEPI_CONDA="flepimop-env"
+    echo "Using '$FLEPI_CONDA' for \$FLEPI_CONDA."
+fi
+
+# Check that the name of the FLEPI_CONDA variable matches the environment that has been set up, exit if not
+FLEPI_CONDA_ENV_MATCHES=$( conda info --envs | awk '{print $1}' | grep -x "$FLEPI_CONDA" | wc -l )
+if [ "$FLEPI_CONDA_ENV_MATCHES" -eq 0 ]; then
+    conda env create --name flepimop-env --file $FLEPI_PATH/environment.yml
+fi
+
+# Load the conda environment
+eval "$(conda shell.bash hook)"
+conda activate $FLEPI_CONDA
+[ -e "$CONDA_PREFIX/conda-meta/pinned" ] && rm $CONDA_PREFIX/conda-meta/pinned
+cat << EOF > $CONDA_PREFIX/conda-meta/pinned
+r-arrow==17.0.0
+arrow==17.0.0
+EOF
+
+# Install the gempyor package from local
+pip install --editable $FLEPI_PATH/flepimop/gempyor_pkg
+
+# Install the local R packages
+R -e "install.packages('covidcast', repos='https://cloud.r-project.org')"
+RETURNTO=$( pwd )
+cd $FLEPI_PATH/flepimop/R_packages/
+for d in $( ls ); do
+    R CMD INSTALL $d
+done
+cd $RETURNTO
+R -e "library(inference); inference::install_cli()"
+
+# Done
+echo "> Done installing/updating flepiMoP."
+set +e

documentation/gitbook/how-to-run/local-installation.md

@@ -0,0 +1,46 @@
+---
+description: >-
+    Instructions on how to proceed with the installations necessary for local flepiMoP use.
+---
+
+
+# Local flepiMoP installation 
+
+## ⇅ Get set up to use Github
+
+You need to interact with Github to run and edit `flepiMoP` code. [Github](https://github.com/) is a web platform for people to share and manage software, and it is based on a 'version control' software called `git` that helps programmers keep track of changes to code. Flepimop core code as well as example projects using flepimop code are all stored on Github, and frequently being updated. The first step to using flepimop for your own project is making sure you're set up to interact with code shared on Github.
+
+If you are totally new to Github, navigate to [Github.com](https://github.com/) and Sign Up for a new account. Read about the [basics of git](https://docs.github.com/en/get-started/getting-started-with-git/set-up-git).
+
+To work with `flepimop` code, you can do some tasks from the Github website, but you'll also need a way to 'clone' the code to your own local computer and keep it up to date with versions hosted online. You can do this either using a user interface like [Github Desktop](https://desktop.github.com/), or, using [`git` ](https://git-scm.com/downloads)commands from the command line. Make sure you have one or both installed.
+
+If you are a veteran user, make sure you're signed in on Github.com and through whatever method you use locally on your computer to interact with Github.
+
+## 🔐 Access the flepiMoP model code
+
+In order to run a model with flepiMoP, you will need to clone the flepiMoP **code** to your machine. 
+
+**To clone the `flepiMoP` code repository:**
+
+* If you're using the command line in a terminal, first navigate to the local directory you'll use as the directory for the files that make up `flepiMoP`. Then, use the command: `git clone https://github.com/HopkinsIDD/flepiMoP`
+* If you're using Github Desktop, go File -> Clone Repository, switch to the "URL" tab and copy the URL `https://github.com/HopkinsIDD/flepiMoP` there. For the "Local Path" option, make sure you choose your desired directory.
+
+## 🐍 Installing `conda`
+
+In order to complete `flepiMoP` installation, you must have [`conda`](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html) installed on your machine. `conda` is a tool that will assist you in managing software environments and code packages on your device, and it will be very helpful in ensuring consistent, reproducible environments across different projects. To install `conda` follow [the directions](https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html) according to your operating system. We would recommend selecting the `Anaconda Distribution` installer of `conda`.
+
+Installation of `conda` may take a few minutes.
+
+## ⬇️ Installing flepiMoP packages and dependencies
+
+Navigate to the `flepiMoP` directory and run the following command:
+
+**Note: This installation script is currently only designed for Mac/Linux operating systems. Windows installation script coming soon.**
+```bash
+./build/local_install_or_update
+```
+
+1. Determine `$FLEPI_PATH` and `$FLEPI_CONDA` environment variables
+2. Activate your conda environment
+3. Install `gempyor` and related Python dependencies
+4. Install necessary R packages and dependencies

flepimop/gempyor_pkg/docs/integration_benchmark.ipynb

@@ -410,7 +410,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "07bfd952-5c42-4704-81cc-5de0c917c0ab",
    "metadata": {
     "execution": {
@@ -450,7 +450,7 @@
     "\n",
     "with Timer(\"onerun_SEIR.seeding\"):\n",
     "    initial_conditions = s.initial_conditions.get_from_config(sim_id, modinf=s)\n",
-    "    seeding_data, seeding_amounts = s.seeding.get_from_config(sim_id, modinf=s)\n",
+    "    seeding_data, seeding_amounts = s.get_seeding_data(sim_id)\n",
     "\n",
     "mobility_subpop_indices = s.mobility.indices\n",
     "mobility_data_indices = s.mobility.indptr\n",

flepimop/gempyor_pkg/docs/integration_doc.ipynb

@@ -70,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "96230106-73e3-4681-b562-6a7269513375",
    "metadata": {
     "execution": {
@@ -109,7 +109,7 @@
     "\n",
     "\n",
     "initial_conditions = gempyor_inference.s.initial_conditions.get_from_config(sim_id2write, modinf=gempyor_inference.s)\n",
-    "seeding_data, seeding_amounts = gempyor_inference.s.seeding.get_from_config(sim_id2write, modinf=gempyor_inference.s)\n",
+    "seeding_data, seeding_amounts = gempyor_inference.s.get_seeding_data(sim_id2write)\n",
     "\n",
     "\n",
     "p_draw = gempyor_inference.s.parameters.parameters_quick_draw(\n",

flepimop/gempyor_pkg/docs/interface.ipynb

@@ -169,7 +169,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "id": "63618148-81db-4fe0-9395-7f21878c1372",
    "metadata": {
     "execution": {
@@ -254,20 +254,15 @@
     "\n",
     "### Run every time:\n",
     "with Timer(\"onerun_SEIR.seeding\"):\n",
+    "    seeding_data, seeding_amounts = gempyor_inference.s.get_seeding_data(sim_id2load if load_ID else sim_id2write)\n",
     "    if load_ID:\n",
     "        initial_conditions = gempyor_inference.s.initial_conditions.get_from_file(\n",
     "            sim_id2load, modinf=gempyor_inference.s\n",
     "        )\n",
-    "        seeding_data, seeding_amounts = gempyor_inference.s.seeding.get_from_file(\n",
-    "            sim_id2load, modinf=gempyor_inference.s\n",
-    "        )\n",
     "    else:\n",
     "        initial_conditions = gempyor_inference.s.initial_conditions.get_from_config(\n",
     "            sim_id2write, modinf=gempyor_inference.s\n",
     "        )\n",
-    "        seeding_data, seeding_amounts = gempyor_inference.s.seeding.get_from_config(\n",
-    "            sim_id2write, modinf=gempyor_inference.s\n",
-    "        )\n",
     "\n",
     "with Timer(\"SEIR.parameters\"):\n",
     "    # Draw or load parameters\n",

flepimop/gempyor_pkg/pyproject.toml

@@ -20,6 +20,7 @@ dependencies = [
     "emcee",
     "graphviz",
     "h5py",
+    "Jinja2",
     "matplotlib",
     "numba>=0.53.1",
     "numpy",
@@ -51,7 +52,8 @@ gempyor-simulate = "gempyor.simulate:_deprecated_simulate"
 
 [tool.setuptools]
 package-dir = {"" = "src"}
-include-package-data = false
+include-package-data = true
+package-data = { "gempyor" = ["templates/*.j2"] }
 
 [tool.setuptools.packages.find]
 where = ["src"]