fix file copy path and upgrade mlflow

docker/celery/requirements.txt

@@ -6,7 +6,7 @@ uvicorn~=0.29.0
 python-multipart~=0.0.5
 ijson~=3.1.4
 python-dotenv~=0.20.0
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 typer~=0.7.0

docker/medcat-deid/Dockerfile

@@ -30,7 +30,7 @@ RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
     chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
-    pip install --no-cache-dir -r requirements.txt && \
+    pip install --no-cache-dir -r /app/requirements.txt && \
     python -m spacy download en_core_web_md
 
 WORKDIR /app

docker/medcat-deid/requirements.txt

@@ -6,7 +6,7 @@ uvicorn~=0.29.0
 python-multipart~=0.0.5
 ijson~=3.1.4
 python-dotenv~=0.20.0
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 typer~=0.7.0

docker/medcat-icd10/Dockerfile

@@ -30,7 +30,7 @@ RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
     chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
-    pip install --no-cache-dir -r requirements.txt && \
+    pip install --no-cache-dir -r /app/requirements.txt && \
     python -m spacy download en_core_web_md
 
 WORKDIR /app

docker/medcat-icd10/requirements.txt

@@ -5,7 +5,7 @@ uvicorn~=0.29.0
 python-multipart~=0.0.5
 ijson~=3.1.4
 python-dotenv~=0.20.0
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 typer~=0.7.0

docker/medcat-snomed/Dockerfile

@@ -31,7 +31,7 @@ RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
     chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
-    pip install --no-cache-dir -r requirements.txt && \
+    pip install --no-cache-dir -r /app/requirements.txt && \
     python -m spacy download en_core_web_md
 
 WORKDIR /app

docker/medcat-snomed/requirements.txt

@@ -5,7 +5,7 @@ uvicorn~=0.29.0
 python-multipart~=0.0.5
 ijson~=3.1.4
 python-dotenv~=0.20.0
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 typer~=0.7.0

docker/medcat-umls/Dockerfile

@@ -30,7 +30,7 @@ RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
     chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
-    pip install --no-cache-dir -r requirements.txt && \
+    pip install --no-cache-dir -r /app/requirements.txt && \
     python -m spacy download en_core_web_md
 
 WORKDIR /app

docker/medcat-umls/requirements.txt

@@ -5,7 +5,7 @@ uvicorn~=0.29.0
 python-multipart~=0.0.5
 ijson~=3.1.4
 python-dotenv~=0.20.0
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 typer~=0.7.0

docker/mlflow/models/requirements.txt

@@ -1,4 +1,4 @@
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 setuptools

docker/mlflow/server/crontab.txt

@@ -1 +1 @@
-* * * * * /usr/local/bin/mlflow gc --backend-store-uri ${MLFLOW_BACKEND_STORE_URI}
+0-30 0 * * * /usr/local/bin/mlflow gc --backend-store-uri ${MLFLOW_BACKEND_STORE_URI}

docker/mlflow/server/requirements.txt

@@ -1,4 +1,4 @@
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 setuptools

docker/trf-deid/Dockerfile

@@ -30,7 +30,7 @@ RUN mkdir -p /app/model/model && \
     mkdir -p /app/model/retrained && \
     chown -R $CMS_UID:$CMS_GID /app
 RUN pip install --no-cache-dir -U pip &&\
-    pip install --no-cache-dir -r requirements.txt && \
+    pip install --no-cache-dir -r /app/requirements.txt && \
     python -m spacy download en_core_web_md
 
 WORKDIR /app

docker/trf-deid/requirements.txt

@@ -5,7 +5,7 @@ uvicorn~=0.29.0
 python-multipart~=0.0.5
 ijson~=3.1.4
 python-dotenv~=0.20.0
-mlflow~=2.14.3
+mlflow~=2.16.2
 psycopg2-binary~=2.9.4
 boto3~=1.28.84
 typer~=0.7.0

pyproject.toml

@@ -17,7 +17,7 @@ dependencies = [
     "python-multipart~=0.0.5",
     "ijson~=3.1.4",
     "python-dotenv~=0.20.0",
-    "mlflow~=2.14.3",
+    "mlflow~=2.16.2",
     "psycopg2-binary~=2.9.4",
     "boto3~=1.28.84",
     "typer~=0.12.3",