[DGL-LifeSci] Release Preparation (CI, Docker, Conda build) (#1399)

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* add docs

* Fix style

* Fix lint

* Bug fix

* Fix test

* Update

* Update

* Update

* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

apps/life_sci/python/setup.py

 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import dgllife
-import sys
+import os
 
 from setuptools import find_packages
+from setuptools import setup
 
-if '--inplace' in sys.argv:
-    from distutils.core import setup
-else:
-    from setuptools import setup
+CURRENT_DIR = os.path.dirname(__file__)
+
+def get_lib_path():
+    """Get library path, name and version"""
+     # We can not import `libinfo.py` in setup.py directly since __init__.py
+    # Will be invoked which introduces dependences
+    libinfo_py = os.path.join(CURRENT_DIR, './dgllife/libinfo.py')
+    libinfo = {'__file__': libinfo_py}
+    exec(compile(open(libinfo_py, "rb").read(), libinfo_py, 'exec'), libinfo, libinfo)
+    version = libinfo['__version__']
+
+    return version
+
+VERSION = get_lib_path()
 
 setup(
     name='dgllife',
-    version=dgllife.__version__,
+    version=VERSION,
     description='DGL-based package for Life Science',
     keywords=[
         'pytorch',
@@ -26,9 +36,9 @@ setup(
     packages=[package for package in find_packages()
               if package.startswith('dgllife')],
     install_requires=[
-        'torch>=1'
+        'torch>=1.1'
         'scikit-learn>=0.22.2',
-        'pandas>=0.25.1',
+        'pandas>=0.24.2',
         'requests>=2.22.0',
         'tqdm'
     ],
@@ -36,5 +46,7 @@ setup(
     classifiers=[
         'Development Status :: 3 - Alpha',
         'Programming Language :: Python :: 3',
+        'License :: OSI Approved :: Apache Software License'
     ],
+    license='APACHE'
 )

apps/life_sci/python/update_version.py

+"""
+This is the global script that set the version information of DGL-LifeSci.
+This script runs and update all the locations that related to versions
+List of affected files:
+- app-root/python/dgllife/__init__.py
+- app-root/conda/dgllife/meta.yaml
+"""
+import os
+import re
+
+__version__ = "0.2.0"
+print(__version__)
+
+# Implementations
+def update(file_name, pattern, repl):
+    update = []
+    hit_counter = 0
+    need_update = False
+    for l in open(file_name):
+        result = re.findall(pattern, l)
+        if result:
+            assert len(result) == 1
+            hit_counter += 1
+            if result[0] != repl:
+                l = re.sub(pattern, repl, l)
+                need_update = True
+                print("%s: %s->%s" % (file_name, result[0], repl))
+            else:
+                print("%s: version is already %s" % (file_name, repl))
+
+        update.append(l)
+    if hit_counter != 1:
+        raise RuntimeError("Cannot find version in %s" % file_name)
+
+    if need_update:
+        with open(file_name, "w") as output_file:
+            for l in update:
+                output_file.write(l)
+
+def main():
+    curr_dir = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
+    proj_root = os.path.abspath(os.path.join(curr_dir, ".."))
+    # python path
+    update(os.path.join(proj_root, "python/dgllife/libinfo.py"),
+           r"(?<=__version__ = \")[.0-9a-z]+", __version__)
+    # conda
+    update(os.path.join(proj_root, "conda/dgllife/meta.yaml"),
+           "(?<=version: \")[.0-9a-z]+", __version__)
+
+if __name__ == '__main__':
+    main()

apps/life_sci/tests/lint/pylintrc

+[MASTER]
+# Adapted from github.com/dmlc/dgl/tests/lint/pylintrc
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code.
+extension-pkg-whitelist=
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS,_cy2,_cy3,backend,data,contrib
+
+# Add files or directories matching the regex patterns to the blacklist. The
+# regex matches against base names, not paths.
+ignore-patterns=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
+# number of processors available to use.
+jobs=4
+
+# Control the amount of potential inferred values when inferring a single
+# object. This can help the performance when dealing with large functions or
+# complex, nested conditions.
+limit-inference-results=100
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# Specify a configuration file.
+#rcfile=
+
+# When enabled, pylint would attempt to guess common misconfiguration and emit
+# user-friendly hints instead of false-positive error messages.
+suggestion-mode=yes
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+unsafe-load-any-extension=no
+
+
+[MESSAGES CONTROL]
+
+# Only show warnings with the listed confidence levels. Leave empty to show
+# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED.
+confidence=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once). You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use "--disable=all --enable=classes
+# --disable=W".
+disable=design,
+        similarities,
+        no-self-use,
+        attribute-defined-outside-init,
+        locally-disabled,
+        star-args,
+        pointless-except,
+        bad-option-value,
+        global-statement,
+        fixme,
+        suppressed-message,
+        useless-suppression,
+        locally-enabled,
+        import-error,
+        unsubscriptable-object,
+        unbalanced-tuple-unpacking,
+        protected-access,
+        useless-object-inheritance,
+        no-else-return,
+        len-as-condition,
+        cyclic-import,       # disabled due to the inevitable dgl.graph -> dgl.subgraph loop
+        undefined-variable,  # disabled due to C extension (should enable)
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where
+# it should appear only once). See also the "--disable" option for examples.
+enable=c-extension-no-member
+
+
+[REPORTS]
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Template used to display messages. This is a python new-style format string
+# used to format the message information. See doc for all details.
+#msg-template=
+
+# Set the output format. Available formats are text, parseable, colorized, json
+# and msvs (visual studio). You can also give a reporter class, e.g.
+# mypackage.mymodule.MyReporterClass.
+output-format=text
+
+# Tells whether to display a full report or only the messages.
+reports=no
+
+# Activate the evaluation score.
+score=yes
+
+
+[REFACTORING]
+
+# Maximum number of nested blocks for function / method body
+max-nested-blocks=5
+
+# Complete name of functions that never returns. When checking for
+# inconsistent-return-statements if a never returning function is called then
+# it will be considered as an explicit return statement and no message will be
+# printed.
+never-returning-functions=sys.exit
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,
+      XXX,
+      TODO
+
+
+[BASIC]
+
+# Naming style matching correct argument names.
+argument-naming-style=snake_case
+
+# Regular expression matching correct argument names. Overrides argument-
+# naming-style.
+#argument-rgx=
+
+# Naming style matching correct attribute names.
+attr-naming-style=snake_case
+
+# Regular expression matching correct attribute names. Overrides attr-naming-
+# style.
+#attr-rgx=
+
+# Bad variable names which should always be refused, separated by a comma.
+bad-names=foo,
+          bar,
+          baz,
+          toto,
+          tutu,
+          tata
+
+# Naming style matching correct class attribute names.
+class-attribute-naming-style=any
+
+# Regular expression matching correct class attribute names. Overrides class-
+# attribute-naming-style.
+#class-attribute-rgx=
+
+# Naming style matching correct class names.
+class-naming-style=PascalCase
+
+# Regular expression matching correct class names. Overrides class-naming-
+# style.
+#class-rgx=
+
+# Naming style matching correct constant names.
+const-naming-style=UPPER_CASE
+
+# Regular expression matching correct constant names. Overrides const-naming-
+# style.
+#const-rgx=
+
+# Minimum line length for functions/classes that require docstrings, shorter
+# ones are exempt.
+docstring-min-length=-1
+
+# Naming style matching correct function names.
+function-naming-style=snake_case
+
+# Regular expression matching correct function names. Overrides function-
+# naming-style.
+#function-rgx=
+
+# Good variable names which should always be accepted, separated by a comma.
+good-names=i,j,k,u,v,e,n,m,w,x,y,g,G,hg,fn,ex,Run,_
+
+# Include a hint for the correct naming format with invalid-name.
+include-naming-hint=no
+
+# Naming style matching correct inline iteration names.
+inlinevar-naming-style=any
+
+# Regular expression matching correct inline iteration names. Overrides
+# inlinevar-naming-style.
+#inlinevar-rgx=
+
+# Naming style matching correct method names.
+method-naming-style=snake_case
+
+# Regular expression matching correct method names. Overrides method-naming-
+# style.
+#method-rgx=
+
+# Naming style matching correct module names.
+module-naming-style=snake_case
+
+# Regular expression matching correct module names. Overrides module-naming-
+# style.
+#module-rgx=
+
+# Colon-delimited sets of names that determine each other's naming style when
+# the name regexes allow several styles.
+name-group=
+
+# Regular expression which should only match function or class names that do
+# not require a docstring.
+no-docstring-rgx=^_
+
+# List of decorators that produce properties, such as abc.abstractproperty. Add
+# to this list to register other decorators that produce valid properties.
+# These decorators are taken in consideration only for invalid-name.
+property-classes=abc.abstractproperty
+
+# Naming style matching correct variable names.
+variable-naming-style=snake_case
+
+# Regular expression matching correct variable names. Overrides variable-
+# naming-style.
+#variable-rgx=
+
+
+[VARIABLES]
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid defining new builtins when possible.
+additional-builtins=
+
+# Tells whether unused global variables should be treated as a violation.
+allow-global-unused-variables=yes
+
+# List of strings which can identify a callback function by name. A callback
+# name must start or end with one of those strings.
+callbacks=cb_,
+          _cb
+
+# A regular expression matching the name of dummy variables (i.e. expected to
+# not be used).
+dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore.
+ignored-argument-names=_.*|^ignored_|^unused_
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# List of qualified module names which can have objects that can redefine
+# builtins.
+redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io
+
+
+[SPELLING]
+
+# Limits count of emitted suggestions for spelling mistakes.
+max-spelling-suggestions=4
+
+# Spelling dictionary name. Available dictionaries: none. To make it working
+# install python-enchant package..
+spelling-dict=
+
+# List of comma separated words that should not be checked.
+spelling-ignore-words=
+
+# A path to a file that contains private dictionary; one word per line.
+spelling-private-dict-file=
+
+# Tells whether to store unknown words to indicated private dictionary in
+# --spelling-private-dict-file option instead of raising a message.
+spelling-store-unknown-words=no
+
+
+[LOGGING]
+
+# Format style used to check logging format string. `old` means using %
+# formatting, while `new` is for `{}` formatting.
+logging-format-style=old
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format.
+logging-modules=logging
+
+
+[FORMAT]
+
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+expected-line-ending-format=
+
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines=^\s*(# )?<?https?://\S+>?$
+
+# Number of spaces of indent required inside a hanging or continued line.
+indent-after-paren=4
+
+# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
+# tab).
+indent-string='    '
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module.
+max-module-lines=4000
+
+# List of optional constructs for which whitespace checking is disabled. `dict-
+# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
+# `trailing-comma` allows a space between comma and closing bracket: (a, ).
+# `empty-line` allows space-only lines.
+no-space-check=trailing-comma,
+               dict-separator
+
+# Allow the body of a class to be on the same line as the declaration if body
+# contains single statement.
+single-line-class-stmt=no
+
+# Allow the body of an if to be on the same line as the test if there is no
+# else.
+single-line-if-stmt=no
+
+
+[SIMILARITIES]
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+
+[TYPECHECK]
+
+# List of decorators that produce context managers, such as
+# contextlib.contextmanager. Add to this list to register other decorators that
+# produce valid context managers.
+contextmanager-decorators=contextlib.contextmanager
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E1101 when accessed. Python regular
+# expressions are accepted.
+generated-members=
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# Tells whether to warn about missing members when the owner of the attribute
+# is inferred to be None.
+ignore-none=yes
+
+# This flag controls whether pylint should warn about no-member and similar
+# checks whenever an opaque object is returned when inferring. The inference
+# can return multiple potential results while evaluating a Python object, but
+# some branches might not be evaluated, which results in partial inference. In
+# that case, it might be useful to still emit no-member and other checks for
+# the rest of the inferred objects.
+ignore-on-opaque-inference=yes
+
+# List of class names for which member attributes should not be checked (useful
+# for classes with dynamically set attributes). This supports the use of
+# qualified names.
+ignored-classes=optparse.Values,thread._local,_thread._local
+
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis. It
+# supports qualified module names, as well as Unix pattern matching.
+ignored-modules=dgl.backend,dgl._api_internal
+
+# Show a hint with possible names when a member name was not found. The aspect
+# of finding the hint is based on edit distance.
+missing-member-hint=yes
+
+# The minimum edit distance a name should have in order to be considered a
+# similar match for a missing member name.
+missing-member-hint-distance=1
+
+# The total number of similar names that should be taken in consideration when
+# showing a hint for a missing member.
+missing-member-max-choices=1
+
+
+[IMPORTS]
+
+# Allow wildcard imports from modules that define __all__.
+allow-wildcard-with-all=yes
+
+# Analyse import fallback blocks. This can be used to support both Python 2 and
+# 3 compatible code, which means that the block might have code that exists
+# only in one or another interpreter, leading to false positives when analysed.
+analyse-fallback-blocks=no
+
+# Deprecated modules which should not be used, separated by a comma.
+deprecated-modules=optparse,tkinter.tix
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled).
+ext-import-graph=
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled).
+import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled).
+int-import-graph=
+
+# Force import order to recognize a module as part of the standard
+# compatibility libraries.
+known-standard-library=
+
+# Force import order to recognize a module as part of a third party library.
+known-third-party=enchant
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method.
+max-args=5
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Maximum number of boolean expressions in an if statement.
+max-bool-expr=5
+
+# Maximum number of branch for function / method body.
+max-branches=12
+
+# Maximum number of locals for function / method body.
+max-locals=15
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+# Maximum number of return / yield for function / method body.
+max-returns=6
+
+# Maximum number of statements in function / method body.
+max-statements=50
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+
+[CLASSES]
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,
+                      __new__,
+                      setUp
+
+# List of member names, which should be excluded from the protected access
+# warning.
+exclude-protected=_asdict,
+                  _fields,
+                  _replace,
+                  _source,
+                  _make
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg=cls
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception".
+overgeneral-exceptions=Exception
\ No newline at end of file

apps/life_sci/tests/model/test_gnn.py

@@ -81,7 +81,7 @@ def test_gat():
     bg, batch_node_feats = bg.to(device), batch_node_feats.to(device)
 
     # Test default setting
-    gnn = GAT(in_feats=1)
+    gnn = GAT(in_feats=1).to(device)
     assert gnn(g, node_feats).shape == torch.Size([3, 32])
     assert gnn(bg, batch_node_feats).shape == torch.Size([8, 32])
 
@@ -196,7 +196,7 @@ def test_mpnn_gnn():
 
     # Test default setting
     gnn = MPNNGNN(node_in_feats=1,
-                  edge_in_feats=2)
+                  edge_in_feats=2).to(device)
     assert gnn(g, node_feats, edge_feats).shape == torch.Size([3, 64])
     assert gnn(bg, batch_node_feats, batch_edge_feats).shape == torch.Size([8, 64])
 
@@ -223,7 +223,7 @@ def test_wln():
 
     # Test default setting
     gnn = WLN(node_in_feats=1,
-              edge_in_feats=2)
+              edge_in_feats=2).to(device)
     assert gnn(g, node_feats, edge_feats).shape == torch.Size([3, 300])
     assert gnn(bg, batch_node_feats, batch_edge_feats).shape == torch.Size([8, 300])
 
@@ -231,7 +231,7 @@ def test_wln():
     gnn = WLN(node_in_feats=1,
               edge_in_feats=2,
               node_out_feats=3,
-              n_layers=1)
+              n_layers=1).to(device)
     assert gnn(g, node_feats, edge_feats).shape == torch.Size([3, 3])
     assert gnn(bg, batch_node_feats, batch_edge_feats).shape == torch.Size([8, 3])
 

apps/life_sci/tests/model/test_property_prediction.py

 import dgl
 import torch
+import torch.nn.functional as F
 
 from dgl import DGLGraph
 
@@ -65,7 +66,7 @@ def test_gcn_predictor():
     bg, batch_node_feats = bg.to(device), batch_node_feats.to(device)
 
     # Test default setting
-    gcn_predictor = GCNPredictor(in_feats=1)
+    gcn_predictor = GCNPredictor(in_feats=1).to(device)
     gcn_predictor.eval()
     assert gcn_predictor(g, node_feats).shape == torch.Size([1, 1])
     gcn_predictor.train()
@@ -213,7 +214,7 @@ def test_mpnn_predictor():
 
     # Test default setting
     mpnn_predictor = MPNNPredictor(node_in_feats=1,
-                                   edge_in_feats=2)
+                                   edge_in_feats=2).to(device)
     assert mpnn_predictor(g, node_feats, edge_feats).shape == torch.Size([1, 1])
     assert mpnn_predictor(bg, batch_node_feats, batch_edge_feats).shape == \
            torch.Size([2, 1])
@@ -226,7 +227,7 @@ def test_mpnn_predictor():
                                    n_tasks=2,
                                    num_step_message_passing=2,
                                    num_step_set2set=2,
-                                   num_layer_set2set=2)
+                                   num_layer_set2set=2).to(device)
     assert mpnn_predictor(g, node_feats, edge_feats).shape == torch.Size([1, 2])
     assert mpnn_predictor(bg, batch_node_feats, batch_edge_feats).shape == \
            torch.Size([2, 2])

apps/life_sci/tests/model/test_reaction_prediction.py

@@ -65,10 +65,10 @@ def test_wln_reaction_center():
     model = WLNReactionCenter(node_in_feats=1,
                               edge_in_feats=2,
                               node_pair_in_feats=1).to(device)
-    assert model(mol_graph, complete_graph, node_feats, edge_feats, atom_pair_feats).shape == \
+    assert model(mol_graph, complete_graph, node_feats, edge_feats, atom_pair_feats)[0].shape == \
            torch.Size([complete_graph.number_of_edges(), 5])
     assert model(batch_mol_graph, batch_complete_graph, batch_node_feats,
-                 batch_edge_feats, batch_atom_pair_feats).shape == \
+                 batch_edge_feats, batch_atom_pair_feats)[0].shape == \
            torch.Size([batch_complete_graph.number_of_edges(), 5])
 
     # Test configured setting
@@ -78,10 +78,10 @@ def test_wln_reaction_center():
                               node_out_feats=1,
                               n_layers=1,
                               n_tasks=1).to(device)
-    assert model(mol_graph, complete_graph, node_feats, edge_feats, atom_pair_feats).shape == \
+    assert model(mol_graph, complete_graph, node_feats, edge_feats, atom_pair_feats)[0].shape == \
            torch.Size([complete_graph.number_of_edges(), 1])
     assert model(batch_mol_graph, batch_complete_graph, batch_node_feats,
-                 batch_edge_feats, batch_atom_pair_feats).shape == \
+                 batch_edge_feats, batch_atom_pair_feats)[0].shape == \
            torch.Size([batch_complete_graph.number_of_edges(), 1])
 
 if __name__ == '__main__':

apps/life_sci/tests/scripts/build.sh

+#!/bin/bash
+
+# Argument
+#  - dev: cpu or gpu
+if [ $# -ne 1 ]; then
+    echo "Device argument required, can be cpu or gpu"
+    exit -1
+fi
+
+dev=$1
+
+set -e
+. /opt/conda/etc/profile.d/conda.sh
+
+rm -rf _deps
+mkdir _deps
+pushd _deps
+conda activate "pytorch-ci"
+if [ "$dev" == "gpu" ]; then
+  pip uninstall -y dgl
+  pip install --pre dgl
+  python3 setup.py install
+else
+  pip uninstall -y dgl-cu101
+  pip install --pre dgl-cu101
+  python3 setup.py install
+fi
+popd
\ No newline at end of file

apps/life_sci/tests/scripts/task_lint.sh

+#!/bin/bash
+# Adapted from github.com/dmlc/dgl/tests/scripts/task_lint.sh
+
+# pylint
+echo 'Checking code style of python codes...'
+python3 -m pylint --reports=y -v --rcfile=tests/lint/pylintrc python/dgllife || exit 1
\ No newline at end of file

apps/life_sci/tests/scripts/task_unit_test.sh

+#!/bin/bash
+
+. /opt/conda/etc/profile.d/conda.sh
+
+function fail {
+    echo FAIL: $@
+    exit -1
+}
+
+function usage {
+    echo "Usage: $0 backend device"
+}
+
+if [ $# -ne 2 ]; then
+    usage
+    fail "Error: must specify backend and device"
+fi
+
+export DGLBACKEND=$1
+export PYTHONPATH=${PWD}/python:$PYTHONPATH
+export DGL_DOWNLOAD_DIR=${PWD}
+
+if [ $2 == "gpu" ]
+then
+  export CUDA_VISIBLE_DEVICES=0
+else
+  export CUDA_VISIBLE_DEVICES=-1
+fi
+
+conda activate ${DGLBACKEND}-ci
+pip install _deps/dgl*.whl
+
+python3 -m pytest -v --junitxml=pytest_data.xml tests/data || fail "data"
+python3 -m pytest -v --junitxml=pytest_model.xml tests/model || fail "model"
+python3 -m pytest -v --junitxml=pytest_utils.xml tests/utils || fail "utils"
\ No newline at end of file

apps/life_sci/tests/utils/test_complex_to_graph.py

@@ -37,8 +37,8 @@ def test_acnn_graph_construction_and_featurization():
                                                   pocket_mol,
                                                   ligand_coords,
                                                   pocket_coords)
-    assert g.ntypes == ['protein_atom', 'ligand_atom']
-    assert g.etypes == ['protein', 'ligand', 'complex', 'complex', 'complex', 'complex']
+    assert set(g.ntypes) == set(['protein_atom', 'ligand_atom'])
+    assert set(g.etypes) == set(['protein', 'ligand', 'complex', 'complex', 'complex', 'complex'])
     assert g.number_of_nodes('protein_atom') == 286
     assert g.number_of_nodes('ligand_atom') == 21
 

apps/life_sci/tests/utils/test_eval.py

@@ -61,22 +61,14 @@ def test_Meter():
     meter = Meter(label_mean, label_std)
     meter.update(label, pred)
     true_scores = [0.22125875529784111, 0.5937311018897714]
-    assert meter.rmse() == true_scores
-    assert meter.rmse('mean') == np.mean(true_scores)
-    assert meter.rmse('sum') == np.sum(true_scores)
-    assert meter.compute_metric('rmse') == true_scores
-    assert meter.compute_metric('rmse', 'mean') == np.mean(true_scores)
-    assert meter.compute_metric('rmse', 'sum') == np.sum(true_scores)
+    assert torch.allclose(torch.tensor(meter.rmse()), torch.tensor(true_scores))
+    assert torch.allclose(torch.tensor(meter.compute_metric('rmse')), torch.tensor(true_scores))
 
     meter = Meter(label_mean, label_std)
     meter.update(label, pred, mask)
     true_scores = [0.1337071188699867, 0.5019903799993205]
-    assert meter.rmse() == true_scores
-    assert meter.rmse('mean') == np.mean(true_scores)
-    assert meter.rmse('sum') == np.sum(true_scores)
-    assert meter.compute_metric('rmse') == true_scores
-    assert meter.compute_metric('rmse', 'mean') == np.mean(true_scores)
-    assert meter.compute_metric('rmse', 'sum') == np.sum(true_scores)
+    assert torch.allclose(torch.tensor(meter.rmse()), torch.tensor(true_scores))
+    assert torch.allclose(torch.tensor(meter.compute_metric('rmse')), torch.tensor(true_scores))
 
     # roc auc score
     meter = Meter()

apps/life_sci/tests/utils/test_rdkit_utils.py

@@ -3,19 +3,19 @@ import os
 import shutil
 
 from dgl.data.utils import download, _get_dgl_url, extract_archive
-from dgllife.utils.rdkit_utils import get_mol_3D_coordinates, load_molecule
+from dgllife.utils.rdkit_utils import get_mol_3d_coordinates, load_molecule
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
 def test_get_mol_3D_coordinates():
     mol = Chem.MolFromSmiles('CCO')
     # Test the case when conformation does not exist
-    assert get_mol_3D_coordinates(mol) is None
+    assert get_mol_3d_coordinates(mol) is None
 
     # Test the case when conformation exists
     AllChem.EmbedMolecule(mol)
     AllChem.MMFFOptimizeMolecule(mol)
-    coords = get_mol_3D_coordinates(mol)
+    coords = get_mol_3d_coordinates(mol)
     assert isinstance(coords, np.ndarray)
     assert coords.shape == (mol.GetNumAtoms(), 3)