Revision to API v3

.github/workflows/mkdocs_build.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Install packages
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install .[docs] --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+          python3 -m pip install .[docs]
       - name: Build static files
         run: |
           mkdocs build

.github/workflows/mkdocs_deploy.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Install packages
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install .[docs] --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+          python3 -m pip install .[docs]
       - name: Build static files
         run: |
           mkdocs build -d site

README.md

@@ -8,7 +8,7 @@ See documentation at https://emod-hub.github.io/EMOD-Generic-Scripts/ for additi
 
 | Directory | Description |
 | --- | --- |
-| env_Alma9 <br /> env_Amazon2023 <br /> env_Debian13 <br /> env_Fedora42 <br /> env_Rocky9 <br /> env_Ubuntu24 | Definition files for singularity containers with various operating systems. Produces the the EMOD executable, schema, and reporters; creates an environment for running EMOD on COMPS with the python packages available to the embedded python interpreter. All files remain on COMPS and are provided to the various workflows as Asset Collection IDs. |
+| env_Alma10 <br /> env_Amazon2023 <br /> env_Debian13 <br /> env_Fedora42 <br /> env_Rocky10 <br /> env_Ubuntu24 | Definition files for Apptainer containers with various operating systems. Produces the the EMOD executable and schema file; creates an environment for running EMOD on COMPS with the python packages available to the embedded python interpreter. All files remain on COMPS and are provided to the various workflows as Asset Collection IDs. |
 | local_python             | Contains additional python scripts with helper functions common to all of the workflows. |
 | model_covariance01       | [Demonstration simulations for heterogeneity in individual behavior.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_covariance01.html) |
 | model_covid01            | Baseline simulations for SARS-CoV-2 in EMOD. Collab with MvG. |
@@ -36,7 +36,7 @@ To get started:
 
 2. Install requirements:
    ```
-   pip install . --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+   pip install .
    ```
 
 3. Run an experiment (requires COMPS credentials):
@@ -62,7 +62,8 @@ To build the documentation locally, do the following:
 2. Navigate to the root directory of the repo and enter the following
 
     ```
-    pip install .[docs] --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+    pip install .[docs]
+    mkdocs build
     ```
 
 ---------------------

docker/emod_env/Dockerfile

@@ -1,19 +1,16 @@
 FROM ubuntu:24.04
 #
 RUN apt-get update
-RUN apt-get -y install software-properties-common
-RUN apt-get update
-RUN add-apt-repository universe
-RUN apt-get -y upgrade
+RUN apt-get upgrade -y
 #
-RUN apt-get -y install python3
-RUN apt-get -y install python3-pip
-RUN apt-get -y install python3-venv
-RUN apt-get -y install mpich
+RUN apt-get install -y python3
+RUN apt-get install -y python3-pip
+RUN apt-get install -y python3-venv
+RUN apt-get install -y mpich
 #
 RUN apt-get clean
 #
 RUN python3 -m venv py_env
 #
-RUN py_env/bin/pip3 install pip             --upgrade
-RUN py_env/bin/pip3 install emod-api==2.0.1 --extra-index-url https://packages.idmod.org/api/pypi/pypi-production/simple
+RUN py_env/bin/pip3 install pip --upgrade
+RUN py_env/bin/pip3 install emod-api~=3.1

docker/emod_exe/Dockerfile

@@ -1,19 +1,16 @@
 FROM ubuntu:24.04
 #
 RUN apt-get update
-RUN apt-get -y install software-properties-common
-RUN apt-get update
-RUN add-apt-repository universe
-RUN apt-get -y upgrade
+RUN apt-get upgrade -y
 #
-RUN apt-get -y install python3-dev
-RUN apt-get -y install libmpich-dev
-RUN apt-get -y install libsqlite3-dev
-RUN apt-get -y install git
-RUN apt-get -y install libc-dev
-RUN apt-get -y install g++
+RUN apt-get install -y python3-dev
+RUN apt-get install -y libmpich-dev
+RUN apt-get install -y libsqlite3-dev
+RUN apt-get install -y git
+RUN apt-get install -y libc-dev
+RUN apt-get install -y g++
 #
-RUN apt-get -y install scons
+RUN apt-get install -y scons
 #
 RUN apt-get clean
 #

docker/emodpy/Dockerfile

@@ -13,5 +13,5 @@ ENV PY_VENV=/py_env
 RUN python3 -m venv $PY_VENV
 ENV PATH="$PY_VENV/bin:$PATH"
 #
-RUN pip3 install pip             --upgrade
-RUN pip3 install emodpy==2.1.13  --extra-index-url https://packages.idmod.org/api/pypi/pypi-production/simple
+RUN pip3 install pip --upgrade
+RUN pip3 install emodpy~=3.1

docs/bib.md

@@ -1,8 +1,8 @@
 [emod-api]: https://emod-hub.github.io/emod-api/
-[emod-generic]: https://docs.idmod.org/projects/emod-generic/en/latest/parameter-overview.html
+[emod-generic]: https://emod-hub.github.io/EMOD-Generic/
 [emodpy]: https://emod-hub.github.io/emodpy/
-[emodpy-hiv]: https://docs.idmod.org/projects/emodpy-hiv/
-[emodpy-malaria]: https://docs.idmod.org/projects/emodpy-malaria/
+[emodpy-hiv]: https://emod-hub.github.io/emodpy-hiv/
+[emodpy-malaria]: https://emod-hub.github.io/emodpy-malaria/
 [idmod]: https://www.idmod.org/
 [idmtools]: https://docs.idmod.org/projects/idmtools/
 [idmtools_cli]: https://docs.idmod.org/projects/idmtools/en/latest/cli/cli_index.html

docs/getting_started.md

@@ -4,7 +4,7 @@
 
 2. Install requirements via `pip` using the IDM artifactory:
 
-    `pip install . --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple`
+    `pip install .`
 
 3. Run an experiment:
 

environments/Alma10/EMOD_ENV.id

@@ -0,0 +1 @@
+192c46ea-a824-f111-92e2-000d3af5294c::Asset Collection

environments/Alma10/EMOD_ENV_Alma10.def

@@ -0,0 +1,32 @@
+Bootstrap: localimage
+From: Assets/EMOD_OS_Alma10.sif
+
+%post
+    dnf upgrade -y
+
+    dnf install -y python
+    dnf install -y python-pip
+    dnf install -y mpich
+
+    dnf clean all
+
+    python3 -m venv py_env
+    . py_env/bin/activate
+
+    pip install pip --upgrade
+    pip install emod-api~=3.1
+
+%runscript
+
+
+%environment
+
+
+%test
+
+
+%labels
+    Author kfrey@idmod.org
+
+%help
+    Minimal container for running EMOD using emod-api for file support.

environments/Alma10/EMOD_EXE.id

@@ -0,0 +1 @@
+b6f4307b-a824-f111-92e2-000d3af5294c::Asset Collection

environments/Alma9/EMOD_EXE_Alma9.def → environments/Alma10/EMOD_EXE_Alma10.def

@@ -1,15 +1,14 @@
 Bootstrap: localimage
-From: Assets/EMOD_OS_Alma9.sif
+From: Assets/EMOD_OS_Alma10.sif
 
 %post
     dnf upgrade -y
 
-    dnf install python-devel -y
-    dnf install mpich-devel -y
-    dnf install sqlite-devel -y
-    dnf install git -y
-    dnf install glibc-devel -y
-    dnf install gcc-c++ -y
+    dnf install -y python-devel
+    dnf install -y mpich-devel
+    dnf install -y git
+    dnf install -y glibc-devel
+    dnf install -y gcc-c++
 
     dnf clean all
 
@@ -50,4 +49,4 @@ From: Assets/EMOD_OS_Alma9.sif
     Author kfrey@idmod.org
 
 %help
-    Minimal container for building EMOD.
+    Minimal container for building EMOD.

environments/Alma10/EMOD_OS.id

@@ -0,0 +1 @@
+ef5416f0-a724-f111-92e2-000d3af5294c::Asset Collection

environments/Alma9/EMOD_OS_Alma9.def → environments/Alma10/EMOD_OS_Alma10.def

@@ -1,5 +1,5 @@
 Bootstrap: docker
-From: almalinux:9.6
+From: almalinux:10.1
 
 %post
     dnf clean all
@@ -17,4 +17,4 @@ From: almalinux:9.6
     Author kfrey@idmod.org
 
 %help
-    Minimal container. Creates an Asset on COMPS; avoids repeated pull from docker.
+    Minimal container. Creates an Asset on COMPS; avoids repeated pull from docker.

environments/Alma10/EMOD_SCHEMA.id

@@ -0,0 +1 @@
+d2d30190-a824-f111-92e2-000d3af5294c::Asset Collection

environments/Amazon2023/EMOD_ENV.id

@@ -1 +1 @@
-cc36c13e-89a0-f011-aa26-b88303911bc1::Asset Collection
+e53bed08-ab24-f111-92e2-000d3af5294c::Asset Collection

environments/Amazon2023/EMOD_ENV_Amazon2023.def

@@ -4,17 +4,17 @@ From: Assets/EMOD_OS_Amazon2023.sif
 %post
     dnf upgrade -y
 
-    dnf -y install python
-    dnf -y install python-pip
-    dnf -y install mpich
+    dnf install -y python3.13
+    dnf install -y python3.13-pip
+    dnf install -y mpich
 
     dnf clean all
 
-    python3 -m venv py_env
+    python3.13 -m venv py_env
     . py_env/bin/activate
 
-    pip install pip              --upgrade
-    pip install emod-api==2.0.26 --extra-index-url https://packages.idmod.org/api/pypi/pypi-production/simple
+    pip install pip --upgrade
+    pip install emod-api~=3.1
 
 %runscript
 
@@ -29,4 +29,4 @@ From: Assets/EMOD_OS_Amazon2023.sif
     Author kfrey@idmod.org
 
 %help
-    Minimal container for running EMOD using emod-api for file support.
+    Minimal container for running EMOD using emod-api for file support.

environments/Amazon2023/EMOD_EXE.id

@@ -1 +1 @@
-b1eb93ae-84a0-f011-aa26-b88303911bc1::Asset Collection
+9cb7f0bf-aa24-f111-92e2-000d3af5294c::Asset Collection

environments/Amazon2023/EMOD_EXE_Amazon2023.def

@@ -4,26 +4,21 @@ From: Assets/EMOD_OS_Amazon2023.sif
 %post
     dnf upgrade -y
 
-    dnf install python-devel -y
-    dnf install mpich-devel -y
-    dnf install sqlite-devel -y
-    dnf install git -y
-    dnf install glibc-devel -y
-    dnf install gcc-c++ -y
+    dnf install -y python3.13-devel
+    dnf install -y python3.13-pip
+    dnf install -y mpich-devel
+    dnf install -y git
+    dnf install -y glibc-devel
+    dnf install -y gcc-c++
 
     dnf clean all
 
-    curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
-    python3 get-pip.py
-    rm get-pip.py
-
-    python3 -m pip install pip --upgrade
-    python3 -m pip install scons
+    python3.13 -m pip install pip --upgrade
+    python3.13 -m pip install scons
 
     export USER=CalculonUser-EMOD
 
     export PATH=$PATH:/usr/lib64/mpich/bin
-    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpich/lib
 
     git clone https://github.com/EMOD-Hub/EMOD-Generic
 
@@ -53,4 +48,4 @@ From: Assets/EMOD_OS_Amazon2023.sif
     Author kfrey@idmod.org
 
 %help
-    Minimal container for building EMOD.
+    Minimal container for building EMOD.

environments/Amazon2023/EMOD_OS.id

@@ -1 +1 @@
-106d5f01-84a0-f011-aa26-b88303911bc1::Asset Collection
+74769f14-aa24-f111-92e2-000d3af5294c::Asset Collection

environments/Amazon2023/EMOD_OS_Amazon2023.def

@@ -17,4 +17,4 @@ From: amazonlinux:2023
     Author kfrey@idmod.org
 
 %help
-    Minimal container. Creates an Asset on COMPS; avoids repeated pull from docker.
+    Minimal container. Creates an Asset on COMPS; avoids repeated pull from docker.

environments/Amazon2023/EMOD_SCHEMA.id

@@ -1 +1 @@
-f670dabc-84a0-f011-aa26-b88303911bc1::Asset Collection
+a113c0d3-aa24-f111-92e2-000d3af5294c::Asset Collection

environments/Debian13/EMOD_ENV.id

@@ -1 +1 @@
-9609789d-8df6-f011-aa29-b88303911bc1::Asset Collection
+55dff54e-ac24-f111-92e2-000d3af5294c::Asset Collection