Archiving the project (#192)

* Adding gitattributes file * Updating gitattributes * Adding the artifact * Adding all 51 artifacts, updates to Readme and model specs * Updating artifact files * Reverting to old artifacts, editing files to have 3 example states * Returning to Jim's new files since Steve fixed the vivarium function * update vph pin * Update README.rst to include model spec file name * Update .zenodo.json with author information * Update README.rst to include artifact path on the command line * Commenting out the artifact path in model spec Since its now in the command line call instead * Update setup.py to include == Co-authored-by: Rajan Mudambi <[email protected]> * Update .zenodo.json to include Matt and Kjell --------- Co-authored-by: Sylvia Lutze <[email protected]> Co-authored-by: Sylvia Lutze <[email protected]> Co-authored-by: Sylvia Lutze <[email protected]> Co-authored-by: Sylvia Lutze <[email protected]> Co-authored-by: Steve Bachmeier <[email protected]> Co-authored-by: Rajan Mudambi <[email protected]>
ihmeuw · Feb 16, 2024 · 2c981cb · 2c981cb
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+*.hdf filter=lfs diff=lfs merge=lfs -text
+**/*.hdf filter=lfs diff=lfs merge=lfs -text
diff --git a/.zenodo.json b/.zenodo.json
@@ -3,12 +3,52 @@
     "title": "ihmeuw/vivarium_nih_us_cvd: Archival release",
     "upload_type": "software",
     "creators": [
-//        {
-//            "orcid": "0000-0000-0000-0000",
-//            "affiliation": "Institute for Health Metrics and Evaluation",
-//            "name": "TODO: Add authors names, affiliation, and orcid (if applicable) to `creators` array"
-//        }
+        {
+            "orcid": "0000-0001-8649-7561",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Rajan Mudambi"
+        },
+        {
+            "orcid": "0009-0004-6649-7010",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Steve Bachmeier"
+        },
+        {
+            "orcid": "0000-0002-7556-2740",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Hussain Jafari"
+        },
+        {
+          "orcid": "0000-0003-0778-295X",
+          "affiliation": "Institute for Health Metrics and Evaluation",
+          "name": "Kjell Swedin"
+        },
+        {
+          "orcid": "0000-0003-2430-5661",
+          "affiliation": "Institute for Health Metrics and Evaluation",
+          "name": "Matthew Kappel"
+        },
+        {
+            "orcid": "0009-0005-7858-0222",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Sylvia Lutze"
+        },
+        {
+            "orcid": "0000-0003-1585-5100",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Alison Bowman"
+        },
+        {
+            "orcid": "0009-0009-3789-5382",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Caroline Kinuthia"
+        },
+        {
+            "orcid": "0000-0001-6033-4713",
+            "affiliation": "Institute for Health Metrics and Evaluation",
+            "name": "Abraham Flaxman"
+        }
     ],
     "access_right": "open",
     "description": "<p>TODO: add description (e.g., Archival release of simulation software.)</p>"
-}
+}
diff --git a/README.rst b/README.rst
@@ -103,22 +103,16 @@ You'll find six directories inside the main
 Running Simulations
 -------------------
 
-With your conda environment active, the first step to running simulations
-is making the model specification files.  A model specification is a
-complete description of a vivarium model. The command to generate model
-specifications is installed with this repository and it can be run
-from any directory.::
+You can run your simulation from the command line. 
+With your conda environment active, you can run with, e.g.::
 
-  (vivarium_nih_us_cvd) :~$ make_specs -v
-  2020-06-18 18:18:28.311 | 0:00:00.679701 | build_model_specifications:48 - Writing model spec(s) to "/REPO_INSTALLATION_DIRECTORY/vivarium_nih_us_cvd/src/vivarium_nih_us_cvd/model_specifications"
+   (vivarium_nih_us_cvd) :~$ simulate run -vvv /<REPO_INSTALLATION_DIRECTORY>/vivarium_nih_us_cvd/src/vivarium_nih_us_cvd/model_specifications/nih_us_cvd.yaml -o /FILE/PATH/TO/SAVE/RESULTS -i src/vivarium_nih_us_cvd/artifacts/<STATE_NAME>.hdf
 
-As the log message indicates, the model specifications will be written to
-the ``model_specifications`` subdirectory in this repository. You can then
-run simulations by, e.g.::
+The simulation will run in one location at a time, enter the state you wish to 
+run the simulation for in your call. The state name should be in lower case with 
+an underscore between words. For example 'alabama', 'new_jersey' and 'district_of_columbia'.  
 
-   (vivarium_nih_us_cvd) :~$ simulate run -v /<REPO_INSTALLATION_DIRECTORY>/vivarium_nih_us_cvd/src/vivarium_nih_us_cvd/model_specifications/china.yaml
-
-The ``-v`` flag will log verbosely, so you will get log messages every time
+The ``-vvv`` flag will log verbosely, so you will get log messages every time
 step. For more ways to run simulations, see the tutorials at
 https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html
-and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html
+and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html
diff --git a/setup.py b/setup.py
@@ -45,7 +45,7 @@
     install_requirements = [
         "gbd_mapping>=3.1.0, <4.0.0",
         "vivarium>=2.1.1",
-        "vivarium_public_health>=2.0.0",
+        "vivarium_public_health==2.2.0",
         "click",
         "jinja2",
         "loguru",

diff --git a/src/vivarium_nih_us_cvd/artifacts/alabama.hdf b/src/vivarium_nih_us_cvd/artifacts/alabama.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/alaska.hdf b/src/vivarium_nih_us_cvd/artifacts/alaska.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/arizona.hdf b/src/vivarium_nih_us_cvd/artifacts/arizona.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/arkansas.hdf b/src/vivarium_nih_us_cvd/artifacts/arkansas.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/california.hdf b/src/vivarium_nih_us_cvd/artifacts/california.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/colorado.hdf b/src/vivarium_nih_us_cvd/artifacts/colorado.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/connecticut.hdf b/src/vivarium_nih_us_cvd/artifacts/connecticut.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/delaware.hdf b/src/vivarium_nih_us_cvd/artifacts/delaware.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/district_of_columbia.hdf b/src/vivarium_nih_us_cvd/artifacts/district_of_columbia.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/florida.hdf b/src/vivarium_nih_us_cvd/artifacts/florida.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/georgia.hdf b/src/vivarium_nih_us_cvd/artifacts/georgia.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/hawaii.hdf b/src/vivarium_nih_us_cvd/artifacts/hawaii.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/idaho.hdf b/src/vivarium_nih_us_cvd/artifacts/idaho.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/illinois.hdf b/src/vivarium_nih_us_cvd/artifacts/illinois.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/indiana.hdf b/src/vivarium_nih_us_cvd/artifacts/indiana.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/iowa.hdf b/src/vivarium_nih_us_cvd/artifacts/iowa.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/kansas.hdf b/src/vivarium_nih_us_cvd/artifacts/kansas.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/kentucky.hdf b/src/vivarium_nih_us_cvd/artifacts/kentucky.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/louisiana.hdf b/src/vivarium_nih_us_cvd/artifacts/louisiana.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/maine.hdf b/src/vivarium_nih_us_cvd/artifacts/maine.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/maryland.hdf b/src/vivarium_nih_us_cvd/artifacts/maryland.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/massachusetts.hdf b/src/vivarium_nih_us_cvd/artifacts/massachusetts.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/michigan.hdf b/src/vivarium_nih_us_cvd/artifacts/michigan.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/minnesota.hdf b/src/vivarium_nih_us_cvd/artifacts/minnesota.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/mississippi.hdf b/src/vivarium_nih_us_cvd/artifacts/mississippi.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/missouri.hdf b/src/vivarium_nih_us_cvd/artifacts/missouri.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/montana.hdf b/src/vivarium_nih_us_cvd/artifacts/montana.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/nebraska.hdf b/src/vivarium_nih_us_cvd/artifacts/nebraska.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/nevada.hdf b/src/vivarium_nih_us_cvd/artifacts/nevada.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/new_hampshire.hdf b/src/vivarium_nih_us_cvd/artifacts/new_hampshire.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/new_jersey.hdf b/src/vivarium_nih_us_cvd/artifacts/new_jersey.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/new_mexico.hdf b/src/vivarium_nih_us_cvd/artifacts/new_mexico.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/new_york.hdf b/src/vivarium_nih_us_cvd/artifacts/new_york.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/north_carolina.hdf b/src/vivarium_nih_us_cvd/artifacts/north_carolina.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/north_dakota.hdf b/src/vivarium_nih_us_cvd/artifacts/north_dakota.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/ohio.hdf b/src/vivarium_nih_us_cvd/artifacts/ohio.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/oklahoma.hdf b/src/vivarium_nih_us_cvd/artifacts/oklahoma.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/oregon.hdf b/src/vivarium_nih_us_cvd/artifacts/oregon.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/pennsylvania.hdf b/src/vivarium_nih_us_cvd/artifacts/pennsylvania.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/rhode_island.hdf b/src/vivarium_nih_us_cvd/artifacts/rhode_island.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/south_carolina.hdf b/src/vivarium_nih_us_cvd/artifacts/south_carolina.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/south_dakota.hdf b/src/vivarium_nih_us_cvd/artifacts/south_dakota.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/tennessee.hdf b/src/vivarium_nih_us_cvd/artifacts/tennessee.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/texas.hdf b/src/vivarium_nih_us_cvd/artifacts/texas.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/utah.hdf b/src/vivarium_nih_us_cvd/artifacts/utah.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/vermont.hdf b/src/vivarium_nih_us_cvd/artifacts/vermont.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/virginia.hdf b/src/vivarium_nih_us_cvd/artifacts/virginia.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/washington.hdf b/src/vivarium_nih_us_cvd/artifacts/washington.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/west_virginia.hdf b/src/vivarium_nih_us_cvd/artifacts/west_virginia.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/wisconsin.hdf b/src/vivarium_nih_us_cvd/artifacts/wisconsin.hdf
diff --git a/src/vivarium_nih_us_cvd/artifacts/wyoming.hdf b/src/vivarium_nih_us_cvd/artifacts/wyoming.hdf
diff --git a/src/vivarium_nih_us_cvd/constants/paths.py b/src/vivarium_nih_us_cvd/constants/paths.py
@@ -7,7 +7,7 @@
 BASE_DIR = Path(vivarium_nih_us_cvd.__file__).resolve().parent
 BASE_OUTPUT_DIR = Path("/mnt/team/simulation_science/pub/models/")
 
-ARTIFACT_ROOT = BASE_OUTPUT_DIR / metadata.PROJECT_NAME / "artifacts"
+ARTIFACT_ROOT = BASE_DIR / "artifacts" 
 DATA_ROOT = BASE_DIR / "data"
 
 CAUSE_RISK_CONFIG = BASE_DIR / "components" / "causes" / "causes.yaml"

diff --git a/src/vivarium_nih_us_cvd/model_specifications/nih_us_cvd.yaml b/src/vivarium_nih_us_cvd/model_specifications/nih_us_cvd.yaml
@@ -89,9 +89,9 @@ components:
 
 
 configuration:
-    # input_data:
-    #     input_draw_number: 0
-    #     artifact_path: '/mnt/team/simulation_science/pub/models/vivarium_nih_us_cvd/artifacts/51-locations/v3-20231019/alabama.hdf'
+    input_data:
+        input_draw_number: 0
+        #artifact_path: '../artifacts/alabama.hdf'
     interpolation:
         order: 0
         extrapolate: True
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		*.hdf filter=lfs diff=lfs merge=lfs -text
		*/.hdf filter=lfs diff=lfs merge=lfs -text