[BBS-292] Release v0.1.0 (#265)

* Remove GitHub Actions workflow to automatically upload to PyPI. * DVC Dockerfiles use versions specified in requirements.txt. * DVC-untrack BSV model, reducing the .dvc/cache to only 4.4 GiB. * Run dvc repro (and dvc push to update the remote storage).
BlueBrain · Mar 4, 2021 · c6dc1fe · c6dc1fe
1 parent 2077dbf
commit c6dc1fe
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diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
diff --git a/data_and_models/models/sentence_embedding/bsv/.gitignore b/data_and_models/models/sentence_embedding/bsv/.gitignore
diff --git a/data_and_models/models/sentence_embedding/bsv/BioSentVec_PubMed_MIMICIII-bigram_d700.bin.dvc b/data_and_models/models/sentence_embedding/bsv/BioSentVec_PubMed_MIMICIII-bigram_d700.bin.dvc
diff --git a/data_and_models/pipelines/ner/Dockerfile b/data_and_models/pipelines/ner/Dockerfile
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-FROM continuumio/miniconda3
+FROM continuumio/miniconda3:4.9.2
 
 ENV HTTP_PROXY='http://bbpproxy.epfl.ch:80/'
 ENV HTTPS_PROXY='http://bbpproxy.epfl.ch:80/'
@@ -29,22 +29,20 @@ RUN true \
 	&& apt-get install -y gcc g++ build-essential vim libfontconfig1 wkhtmltopdf
 RUN conda install -c carta mysqlclient
 
-# Install basis SciSpaCy models
-RUN pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.5/en_ner_jnlpba_md-0.2.5.tar.gz
-RUN pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.5/en_ner_bionlp13cg_md-0.2.5.tar.gz
-RUN pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.5/en_ner_bc5cdr_md-0.2.5.tar.gz
-RUN pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.5/en_ner_craft_md-0.2.5.tar.gz
-
 # Install Prodigy -- assume that we have Prodigy wheel there!
 RUN mkdir -p /bbs/tmp
-COPY prodigy-1.10.4-cp36.cp37.cp38-cp36m.cp37m.cp38-linux_x86_64.whl /bbs/tmp
-RUN pip install /bbs/tmp/prodigy-1.10.4-cp36.cp37.cp38-cp36m.cp37m.cp38-linux_x86_64.whl
+COPY prodigy-1.10.7-cp36.cp37.cp38-cp36m.cp37m.cp38-linux_x86_64.whl /bbs/tmp
+RUN pip install /bbs/tmp/prodigy-1.10.7-cp36.cp37.cp38-cp36m.cp37m.cp38-linux_x86_64.whl
 
 # Instal BlueBrainSearach -- revision can be a branch, sha, or tag
 ARG BBS_REVISION=v0.1.0
 ADD . /src
 WORKDIR /src
-RUN pip install git+file://$PWD@$BBS_REVISION
+RUN git checkout $BBS_REVISION
+# remove ruamel-yaml: https://github.com/pypa/pip/issues/5247#issuecomment-381550610
+RUN rm -rf /opt/conda/lib/python3.8/site-packages/ruamel*
+RUN pip install -r requirements.txt
+RUN pip install $PWD
 
 
 EXPOSE 8888

diff --git a/data_and_models/pipelines/ner/dvc.lock b/data_and_models/pipelines/ner/dvc.lock
@@ -6,8 +6,8 @@ train_model1:
     md5: 613308ed830d86284a1aee2747d911d0
     size: 324136
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: train.py
     md5: 1ccae6b57456b9e5790a0f1232880f4b
     size: 2505
@@ -30,8 +30,8 @@ train_model2:
     md5: 2459e49418599ff96ab9db60a29b757b
     size: 953728
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: train.py
     md5: 1ccae6b57456b9e5790a0f1232880f4b
     size: 2505
@@ -54,8 +54,8 @@ train_model3:
     md5: 4b6fff4b0091fa10ae7c88a4aeb42ae0
     size: 969928
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: train.py
     md5: 1ccae6b57456b9e5790a0f1232880f4b
     size: 2505
@@ -78,8 +78,8 @@ train_model4:
     md5: ec5d6b86181b9e4cdefb2b2198d5ae4f
     size: 267307
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: train.py
     md5: 1ccae6b57456b9e5790a0f1232880f4b
     size: 2505
@@ -102,8 +102,8 @@ train_model5:
     md5: ceb6ea77d2a6a69962b88218f4f5a663
     size: 394725
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: train.py
     md5: 1ccae6b57456b9e5790a0f1232880f4b
     size: 2505
@@ -134,8 +134,8 @@ eval_disease:
     size: 100183520
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -163,8 +163,8 @@ eval_cell_compartment:
     size: 100194437
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -192,8 +192,8 @@ eval_drug:
     size: 100194437
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -220,8 +220,8 @@ eval_organ:
     size: 100194437
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -249,8 +249,8 @@ eval_chemical:
     size: 100228858
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -277,8 +277,8 @@ eval_organism:
     size: 100228858
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -305,8 +305,8 @@ eval_cell_type:
     size: 100215798
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -334,8 +334,8 @@ eval_protein:
     size: 100215798
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -363,8 +363,8 @@ eval_pathway:
     size: 100224717
     nfiles: 18
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: eval.py
     md5: 3c9e86f7cbfaea90929e96a6443a16d4
     size: 3391
@@ -387,8 +387,8 @@ add_er_1:
     size: 100181750
     nfiles: 16
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: add_er.py
     md5: aafbf109663670ded44f84025e4a37a3
     size: 2531
@@ -414,8 +414,8 @@ add_er_2:
     size: 100192674
     nfiles: 16
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: add_er.py
     md5: aafbf109663670ded44f84025e4a37a3
     size: 2531
@@ -445,8 +445,8 @@ add_er_3:
     size: 100227109
     nfiles: 16
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: add_er.py
     md5: aafbf109663670ded44f84025e4a37a3
     size: 2531
@@ -474,8 +474,8 @@ add_er_4:
     size: 100214049
     nfiles: 16
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: add_er.py
     md5: aafbf109663670ded44f84025e4a37a3
     size: 2531
@@ -502,8 +502,8 @@ add_er_5:
     size: 100222954
     nfiles: 16
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: add_er.py
     md5: aafbf109663670ded44f84025e4a37a3
     size: 2531
@@ -534,8 +534,8 @@ interrater:
     md5: 6e248863604ce14861f38e7c9a8281bb
     size: 64285
   - path: Dockerfile
-    md5: c7481f2f16107f71bbba5a4f08e6054e
-    size: 2173
+    md5: da73fa137594c015a32f36ebc772f553
+    size: 1987
   - path: interrater.py
     md5: dd9cabff57a4608753e0777838f9c746
     size: 2984

diff --git a/data_and_models/pipelines/sentence_embedding/Dockerfile b/data_and_models/pipelines/sentence_embedding/Dockerfile
@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
-FROM continuumio/miniconda3
+FROM continuumio/miniconda3:4.9.2
 
 ENV HTTP_PROXY='http://bbpproxy.epfl.ch:80/'
 ENV HTTPS_PROXY='http://bbpproxy.epfl.ch:80/'
@@ -33,7 +33,11 @@ RUN conda install -c carta mysqlclient
 ARG BBS_REVISION=v0.1.0
 ADD . /src
 WORKDIR /src
-RUN pip install git+file://$PWD@$BBS_REVISION
+RUN git checkout $BBS_REVISION
+# remove ruamel-yaml: https://github.com/pypa/pip/issues/5247#issuecomment-381550610
+RUN rm -rf /opt/conda/lib/python3.8/site-packages/ruamel*
+RUN pip install -r requirements.txt
+RUN pip install $PWD
 
 
 EXPOSE 8888