Merge pull request #276 from chemprop/fix-env-gpu

Update default channels in environment.yml and refactor Dockerfile
chemprop · May 13, 2022 · b1f3422 · b1f3422
2 parents e0f644c + d2eb3fa
commit b1f3422
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Showing 4 changed files with 17 additions and 28 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,20 +1,21 @@
-FROM continuumio/miniconda3:4.9.2
+FROM mambaorg/micromamba:0.23.0
 
-COPY environment.yml /tmp/environment.yml
+USER root
 
-RUN /opt/conda/bin/conda env update -n base --file /tmp/environment.yml && \
-    find /opt/conda/ -follow -type f -name '*.a' -delete && \
-    find /opt/conda/ -follow -type f -name '*.js.map' -delete && \
-    /opt/conda/bin/conda clean -afy && \
-    rm /tmp/environment.yml
+RUN apt-get update && \
+    apt-get install -y git && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}
 
-COPY . /opt/chemprop
+USER $MAMBA_USER
 
-WORKDIR /opt/chemprop
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+
+RUN micromamba install -y -n base -f /tmp/environment.yml && \
+    micromamba clean --all --yes
 
-RUN /opt/conda/bin/pip install -e .
+COPY --chown=$MAMBA_USER:$MAMBA_USER . /opt/chemprop
+
+WORKDIR /opt/chemprop
 
-ENV PATH /opt/conda/bin${PATH:+:${PATH}}
+RUN /opt/conda/bin/python -m pip install -e .
 
-ENTRYPOINT ["/bin/bash"]
-CMD ["-l"]
diff --git a/environment.yml b/environment.yml
@@ -1,12 +1,11 @@
 name: chemprop
 
 channels:
-  - conda-forge
   - pytorch
-  - rdkit
+  - conda-forge
 
 dependencies:
-  - python>=3.6
+  - python>=3.7
   - flask>=1.1.2
   - gunicorn>=20.0.4
   - hyperopt>=0.2.3

diff --git a/setup.py b/setup.py
@@ -57,10 +57,9 @@
             'parameterized>=0.8.1'
         ]
     },
-    python_requires='>=3.6',
+    python_requires='>=3.7',
     classifiers=[
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'License :: OSI Approved :: MIT License',

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -259,7 +259,6 @@ def test_train_single_task_regression(self,
                                           expected_score: float,
                                           train_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/train_single_regression/{name}'
             # Train
             self.train(
                 dataset_type='regression',
@@ -327,7 +326,6 @@ def test_train_multi_task_classification(self,
                                              expected_score: float,
                                              train_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/train_multi_class/{name}'
             # Train
             self.train(
                 dataset_type='classification',
@@ -382,7 +380,6 @@ def test_predict_single_task_regression(self,
                                             train_flags: List[str] = None,
                                             predict_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/pred_single_regression/{name}'
             # Train
             dataset_type = 'regression'
             self.train(
@@ -416,7 +413,6 @@ def test_predict_single_task_regression(self,
 
     def test_predict_individual_ensemble(self):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/pred_single_regression/individual_ensemble'
             # Train
             dataset_type = 'regression'
             self.train(
@@ -468,7 +464,6 @@ def test_predict_multi_task_classification(self,
                                                train_flags: List[str] = None,
                                                predict_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/pred_multi_class/{name}'
             # Train
             dataset_type = 'classification'
             self.train(
@@ -502,7 +497,6 @@ def test_predict_multi_task_classification(self,
 
     def test_chemprop_hyperopt(self):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/hyperopt'
             # Train
             config_save_path = os.path.join(save_dir, 'config.json')
             self.hyperopt(
@@ -537,7 +531,6 @@ def test_interpret_single_task_regression(self,
                                               train_flags: List[str] = None,
                                               interpret_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/interpret_single_regression/{name}'
             # Train
             dataset_type = 'regression'
             self.train(
@@ -657,7 +650,6 @@ def test_train_spectra(self,
                                           expected_score: float,
                                           train_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/train_spectra/{name}'
             # Train
             metric = 'sid'
             self.train(
@@ -715,7 +707,6 @@ def test_predict_spectra(self,
                                             train_flags: List[str] = None,
                                             predict_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/pred_spectra/{name}'
             # Train
             dataset_type = 'spectra'
             self.train(
@@ -786,7 +777,6 @@ def test_train_single_task_regression_reaction(self,
                                           expected_score: float,
                                           train_flags: List[str] = None):
         with TemporaryDirectory() as save_dir:
-            save_dir = f'../test/train_single_reaction/{name}'
             # Train
             metric = 'rmse'
             self.train(