Add DOI badge to readme (#127)

* Add zenodo doi badge * Update environment * Add zenodo affliation metadata.
ulissigroup · Jul 2, 2023 · 0c2e0ed · 0c2e0ed
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diff --git a/.gitignore b/.gitignore
@@ -47,3 +47,4 @@ docs/_build/
 !docs/1D_water_PES.png
 !examples/4_misc/predicted_1D_water_PES.png
 !examples/4_misc/water_2d.traj
+!.zenodo.json
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,71 @@
+{
+    "description": "<p>This is the stable initial release with key features.</p>\nMajor features:\n<ul>\n<li>GMP fingerprint support</li>\n<li>PyTorch Geometric integration</li>\n<li>Skorch integration</li>\n<li>GPU/Multi-GPU support via DataParallel</li>\n<li>Weights and Biases logger support</li>\n<li>Uncertainty quantification support</li>\n<li>LMDB data storage option</li>\n</ul>", 
+    "license": "other-open", 
+    "title": "ulissigroup/amptorch: Initial Release", 
+    "version": "v0.2.0-alpha", 
+    "upload_type": "software", 
+    "publication_date": "2023-07-01", 
+    "creators": [
+        {
+            "affiliation": "Department of Chemical Engineering, Carnegie Mellon University", 
+            "name": "Muhammed Shuaibi"
+        }, 
+        {
+            "affiliation": "Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology", 
+            "name": "Xiangyun Lei"
+        }, 
+        {
+            "affiliation": "Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology", 
+            "name": "Yuge Hu"
+        }, 
+        {
+            "affiliation": "Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology", 
+            "name": "Ben Comer"
+        }, 
+        {
+            "affiliation": "Department of Chemical Engineering, Carnegie Mellon University", 
+            "name": "Matt Adams"
+        }, 
+        {
+            "affiliation": "School of Physics and School of Computer Science, Georgia Institute of Technology", 
+            "name": "Jacob Paras"
+        }, 
+        {
+            "affiliation": "Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology", 
+            "name": "Rui Qi Chen"
+        }, 
+        {
+            "affiliation": "Department of Chemical Engineering, University of Michigan",
+            "name": "Eric Musa "
+        }, 
+        {
+            "affiliation": "Department of Chemical Engineering, Carnegie Mellon University", 
+            "name": "Joseph Musielewicz"
+        }, 
+        {
+            "affiliation": "School of Engineering, Brown University", 
+            "name": "Andrew A. Peterson"
+        }, 
+        {
+            "affiliation": "Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology", 
+            "name": "Andrew J. Medford"
+        }, 
+        {
+            "affiliation": "Department of Chemical Engineering, Carnegie Mellon University", 
+            "name": "Zachary Ulissi"
+        }
+    ], 
+    "access_right": "open", 
+    "related_identifiers": [
+        {
+            "scheme": "url", 
+            "identifier": "https://github.com/ulissigroup/amptorch/tree/v0.2.0-alpha", 
+            "relation": "isSupplementTo"
+        }, 
+        {
+            "scheme": "doi", 
+            "identifier": "10.5281/zenodo.8103322", 
+            "relation": "isVersionOf"
+        }
+    ]
+}
diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
-[![ulissigroup](https://circleci.com/gh/ulissigroup/amptorch.svg?style=svg)](https://app.circleci.com/pipelines/github/ulissigroup/amptorch)
+[![ulissigroup](https://circleci.com/gh/ulissigroup/amptorch.svg?style=svg)](https://app.circleci.com/pipelines/github/ulissigroup/amptorch) [![DOI](https://zenodo.org/badge/167388058.svg)](https://zenodo.org/badge/latestdoi/167388058)
+
 ## *AmpTorch*: Atomistic Machine-learning Package - PyTorch
 
 *AmpTorch* is a PyTorch implementation of the [Atomistic Machine-learning Package](https://amp.readthedocs.io/en/latest/) (AMP) code that seeks to provide users with improved performance and flexibility as compared to the original code. The implementation does so by benefiting from state-of-the-art machine learning methods and techniques to be optimized in conjunction with high-throughput supercomputers. *AmpTorch* is built on top of [PyTorch Geometric](https://pytorch-geometric.readthedocs.io/en/latest/) and [Skorch](https://skorch.readthedocs.io/en/stable/).

diff --git a/env_cpu.yml b/env_cpu.yml
@@ -11,7 +11,6 @@ dependencies:
   - pip
   - tqdm=4.45.*
   - cpuonly
-  - numpy=1.20.*
   - pip:
     - ase==3.21.*
     - cffi
@@ -27,3 +26,5 @@ dependencies:
     - -f https://data.pyg.org/whl/torch-1.10.0+cpu.html
     - torch-sparse==0.6.13
     - -f https://data.pyg.org/whl/torch-1.10.0+cpu.html
+    - numpy==1.20.*
+
diff --git a/env_gpu.yml b/env_gpu.yml
@@ -11,7 +11,6 @@ dependencies:
   - matplotlib=3.3.*
   - pip
   - tqdm=4.45.*
-  - numpy=1.20.*
   - pip:
     - ase==3.21.*
     - cffi
@@ -27,3 +26,4 @@ dependencies:
     - -f https://data.pyg.org/whl/torch-1.10.0+cu113.html
     - torch-sparse==0.6.13
     - -f https://data.pyg.org/whl/torch-1.10.0+cu113.html
+    - numpy==1.20.*