updating readme [skip ci]

Dockerfile

@@ -1,9 +1,10 @@
 FROM bentoml/model-server:0.11.0-py37
 MAINTAINER ersilia
 
-RUN conda install -c conda-forge rdkit=2021.03
-RUN conda install -c mordred-descriptor mordred=1.2
+RUN pip install rdkit==2023.3.2 
+RUN pip install mordred==1.2
 RUN pip install timeout-decorator==0.5.0
+RUN pip install pandas==1.3.5
 
 WORKDIR /repo
-COPY ./repo
+COPY ./repo

README.md

@@ -25,6 +25,8 @@ A set of ca 1,800 chemical descriptors, including both RDKit and original module
 
 ## Ersilia model URLs
 * [GitHub](https://github.com/ersilia-os/eos78ao)
+* [AWS S3](https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos78ao.zip)
+* [DockerHub](https://hub.docker.com/r/ersiliaos/eos78ao) (AMD64, ARM64)
 
 ## Citation
 

metadata.json

@@ -26,5 +26,11 @@
     "Publication": "https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0258-y",
     "Source Code": "https://github.com/mordred-descriptor/mordred",
     "License": "BSD-3.0",
-    "Contributor": "miquelduranfrigola"
+    "Contributor": "miquelduranfrigola",
+    "S3": "https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos78ao.zip",
+    "DockerHub": "https://hub.docker.com/r/ersiliaos/eos78ao",
+    "Docker Architecture": [
+        "AMD64",
+        "ARM64"
+    ]
 }

model/framework/run.sh

@@ -0,0 +1 @@
+python $1/code/main.py $2 $3

src/service.py

@@ -45,7 +45,7 @@ def set_checkpoints_dir(self, dest):
     def set_framework_dir(self, dest):
         self.framework_dir = os.path.abspath(dest)
 
-    def calculate(self, smiles_list):
+    def run(self, smiles_list):
         tmp_folder = tempfile.mkdtemp()
         data_file = os.path.join(tmp_folder, self.DATA_FILE)
         pred_file = os.path.join(tmp_folder, self.PRED_FILE)
@@ -57,7 +57,7 @@ def calculate(self, smiles_list):
         run_file = os.path.join(tmp_folder, self.RUN_FILE)
         with open(run_file, "w") as f:
             lines = [
-                "python {0}/calculate.py {1} {2}".format(
+                "bash {0}/run.sh {0} {1} {2}".format(
                     self.framework_dir,
                     data_file,
                     pred_file
@@ -132,8 +132,8 @@ def save(self, dst):
 @artifacts([Artifact("model")])
 class Service(BentoService):
     @api(input=JsonInput(), batch=True)
-    def calculate(self, input: List[JsonSerializable]):
+    def run(self, input: List[JsonSerializable]):
         input = input[0]
         smiles_list = [inp["input"] for inp in input]
-        output = self.artifacts.model.calculate(smiles_list)
+        output = self.artifacts.model.run(smiles_list)
         return [output]