-
Notifications
You must be signed in to change notification settings - Fork 30
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Showing
11 changed files
with
303 additions
and
81 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| #!/bin/bash | ||
| # | ||
| # This script sets up the shell environment for this project. | ||
| # | ||
| # Usage: | ||
| # $ source .env | ||
|
|
||
| export PHD="$(realpath $(dirname "$0"))" | ||
|
|
||
| if [[ -f "$HOME/.cache/phd/tools/py/venv/phd/bin/activate" ]]; then | ||
| # If there is a virtualenv, use it. Note that even if it does exist, bazel | ||
| # will go ahead and ignore it, so we still need to rely on the system python | ||
| # being the required version. | ||
| . "$HOME/.cache/phd/tools/py/venv/phd/bin/activate" | ||
| fi | ||
|
|
||
| # Note(github.com/ChrisCummins/phd/issues/55): On macOS, custom LDFLAGS and | ||
| # CPPFLAGS are required to pip build MySQLdb: | ||
| export LDFLAGS="-L/usr/local/opt/openssl/lib" | ||
| export CPPFLAGS="-I/usr/local/opt/openssl/include" | ||
|
|
||
| # Increase the timeout on docker image pulls from the default 600s. | ||
| # See: https://github.com/bazelbuild/rules_docker | ||
| export PULLER_TIMEOUT=3600 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,216 @@ | ||
| # Python package dependencies. | ||
| # This file is copied to $ROOT/requirements.txt during configure. The reason | ||
| # for this is because the TensorFlow package is replaced with tensorflow-gpu | ||
| # if --with-cuda is enabled. | ||
| absl-py==0.7.0 | ||
| appdirs==1.4.3 | ||
| appnope==0.1.0 | ||
| ascii_art==0.1.0 | ||
| aspy.refactor-imports==1.1.0 | ||
| astroid==1.6.1 | ||
| attrs==19.3.0 | ||
| autoenv==1.0.0 | ||
| backports-abc==0.5 | ||
| backports.functools-lru-cache==1.5 | ||
| backports.shutil-get-terminal-size==1.0.0 | ||
| bibtexparser==1.1.0 | ||
| bleach==1.5.0 | ||
| bokeh==1.0.2 | ||
| cached-property==1.5.1 | ||
| certifi==2018.4.16 # Dependency of requests. | ||
| cffi==1.11.5 | ||
| chardet==3.0.4 # Dependency of requests. | ||
| checksumdir==1.0.5 | ||
| Click==7.0 | ||
| configparser==3.5.0 | ||
| coverage==4.5.1 # Needed by pytest-cov. | ||
| cpplint==1.3.0 | ||
| cycler==0.10.0 | ||
| dash==0.39.0 | ||
| dash-core-components==0.44.0 | ||
| dash-html-components==0.14.0 | ||
| dash-renderer==0.20.0 | ||
| dash-table==3.6.0 | ||
| dataclasses==0.6 | ||
| decorator==4.3.0 | ||
| detect-secrets==0.12.4 | ||
| # The graph_nets package depends on a specific version of dm-sonnet. See: | ||
| # https://github.com/deepmind/graph_nets/blob/master/setup.py | ||
| dm-sonnet==1.23 | ||
| docutils==0.14 | ||
| editdistance==0.3.1 | ||
| entrypoints==0.2.3 | ||
| enum34==1.1.6 | ||
| fasteners==0.15 | ||
| flaky==3.6.1 | ||
| Flask==1.0.2 | ||
| Flask-Compress==1.4.0 | ||
| flask-cors==3.0.6 | ||
| Flask-SQLalchemy==2.4.0 | ||
| fs==2.4.8 | ||
| fs.sshfs==0.11.1 | ||
| funcsigs==1.0.2 | ||
| futures==3.1.1 | ||
| fuzzywuzzy==0.16.0 | ||
| gast==0.2.2. # Dependency of tensorflow. | ||
| GitPython==2.1.11 | ||
| GPUtil==1.4.0 | ||
| graph_nets==1.0.2 | ||
| graphviz==0.9 | ||
| grpcio-tools==1.18.0 | ||
| grpcio==1.18.0 | ||
| gspread==3.1.0 | ||
| gspread-dataframe==3.0.3 | ||
| gym==0.10.5 | ||
| h5py==2.9.0 | ||
| html5lib==0.9999999 | ||
| httplib2==0.14 # Needed by oauth2client | ||
| humanize==0.5.1 | ||
| importlib-metadata==0.23 # Needed by pytest. | ||
| idna==2.6 # Dependency of requests. | ||
| inotify==0.2.10 | ||
| ipaddress==1.0.23 # Dependency of urllib3 | ||
| ipdb==0.11 | ||
| ipykernel==4.8.2 | ||
| ipython-genutils==0.2.0 | ||
| ipython==5.7.0 | ||
| ipywidgets==7.1.2 | ||
| isort==4.3.4 | ||
| itsdangerous==1.1.0 # Dependency of dash. | ||
| jedi==0.11.1 | ||
| jinja2==2.10.1 | ||
| jsonschema==2.6.0 | ||
| jupyter-client==5.2.2 | ||
| jupyter-console==5.2.0 | ||
| jupyter-core==4.4.0 | ||
| jupyter==1.0.0 | ||
| # Support for local runtimes with Google Colaboratory. See: | ||
| # https://research.google.com/colaboratory/local-runtimes.html | ||
| jupyter_http_over_ws==0.0.1a3 | ||
| jwt==0.6.1 # Dependency PyGithub. | ||
| Keras==2.3.1 | ||
| kiwisolver==1.0.1 | ||
| lazy-object-proxy==1.3.1 | ||
| lru-dict==1.1.6 | ||
| MarkupSafe==1.0 | ||
| matplotlib==2.2.0rc1 | ||
| mccabe==0.6.1 | ||
| memory-profiler==0.55.0 | ||
| mistune==0.8.3 | ||
| monotonic==1.5 # Needed by fasteners. | ||
| more-itertools==7.2.0 # Need by pytest. | ||
| mypy-extensions==0.4.3 | ||
| mysqlclient==1.4.2.post1 | ||
| nbconvert==5.3.1 | ||
| nbformat==4.4.0 # Needed by notebook. | ||
| networkx==2.2 | ||
| notebook==5.7.8 | ||
| numpy==1.16.4 | ||
| oauth2client==4.1.3 | ||
| packaging==19.2 # Needed by pytest. | ||
| pandas==0.24.1 | ||
| pandas-bokeh==0.0.2 | ||
| pandocfilters==1.4.2 | ||
| paramiko==2.6.0 # Needed by fs.ssh. | ||
| parso==0.1.1 | ||
| pathlib2==2.3.2 | ||
| pathlib==1.0.1 | ||
| pathspec==0.7.0 | ||
| pexpect==4.4.0 | ||
| pickleshare==0.7.4 | ||
| plotly==3.7.0 | ||
| pluggy==0.13.0 # Needed by pytest. | ||
| ply==3.11 | ||
| portpicker==1.3.1 | ||
| prettytable==0.7.2 | ||
| progressbar2==3.37.1 | ||
| prometheus_client==0.6.0 # Needed by notebook. | ||
| prompt-toolkit==1.0.15 | ||
| property-cached==1.6.3 | ||
| protobuf==3.6.1 | ||
| psutil==5.4.5 | ||
| psycopg2-binary==2.8.3 | ||
| ptyprocess==0.5.2 | ||
| py-cpuinfo==3.3.0 | ||
| py==1.5.2 | ||
| # At the time of writing (2018-05-10), the most recent version of pycparser is | ||
| # version 2.18, however, it breaks cldrive with error: | ||
| # Traceback (most recent call last): | ||
| # File "<snip>/phd/gpu/cldrive/legacy/__init__.py", line 7, in <module> | ||
| # from gpu.cldrive.args import * | ||
| # File "<snip>/phd/gpu/cldrive/legacy/args.py", line 242, in <module> | ||
| # __parser = OpenCLCParser() | ||
| # File "<snip>/site-packages/pycparserext/ext_c_parser.py", line 47, in __init__ | ||
| # debug=yacc_debug, write_tables=False) | ||
| # File "<snip>/site-packages/pycparser/ply/yacc.py", line 3426, in yacc | ||
| # raise YaccError('Unable to build parser') | ||
| # pycparser.ply.yacc.YaccError: Unable to build parser | ||
| pycparser==2.17 | ||
| pycparserext==2016.2 | ||
| pydot==1.4.1 | ||
| PyGithub==1.39 | ||
| Pygments==2.2.0 | ||
| pybind11==2.4.2 # Needed by pyopencl. | ||
| pyfiglet==0.8.post1 | ||
| pylint==1.8.2 | ||
| pyopencl==2018.2.5 | ||
| pyOpenSSL==19.1.0 # Needed by urllib3. | ||
| pyparsing==2.2.0 | ||
| pytest-benchmark==3.2.2 | ||
| pytest-cov==2.8.1 | ||
| pytest-mock==1.12.1 | ||
| pytest-shard==0.1.1 | ||
| pytest==5.3.1 | ||
| python-dateutil==2.6.1 | ||
| python-Levenshtein==0.12.0 | ||
| python-utils==2.3.0 | ||
| python-xmp-toolkit==2.0.1 | ||
| pytools==2018.1 | ||
| pytz==2018.3 | ||
| PyYAML==4.2b4 | ||
| pyzmq==17.0.0 | ||
| pyasn1==0.4.7 # Needed by oauth2client. | ||
| pyasn1_modules==0.2.7 # Needed by oauth2client. | ||
| qtconsole==4.3.1 | ||
| regex==2019.11.1 | ||
| reorder-python-imports==1.9.0 | ||
| requests==2.20.1 | ||
| retrying==1.3.3 # Needed by plotly. | ||
| rsa==4.0 # Needed by oauth2client. | ||
| scandir==1.7 | ||
| scikit-learn==0.20.3 | ||
| scikit-image==0.14.2 | ||
| scipy==1.2.1 | ||
| seaborn==0.9.0 | ||
| Send2Trash==1.5.0 | ||
| simplegeneric==0.8.1 | ||
| singledispatch==3.4.0.3 | ||
| six==1.11.0 # Needed by absl. | ||
| smmap2==2.0.3 | ||
| SQLAlchemy==1.3.10 | ||
| sqlparse==0.3.0 | ||
| statistics==1.0.3.5 | ||
| subprocess32==3.5.0 | ||
| tabulate==0.8.5 | ||
| tensorflow==1.14.0 # NOTE: Must be installed manually with `pip install`. | ||
| terminado==0.8.1 | ||
| testpath==0.3.1 | ||
| TogglPy==0.1.1 | ||
| toml==0.10.0 | ||
| torch==1.3.0 | ||
| tornado==5.0 | ||
| tqdm==4.38.0 | ||
| traitlets==4.3.2 | ||
| trash-cli==0.17.1.14 | ||
| typed-ast==1.4.1 | ||
| typing-extensions==3.7.4.1 | ||
| umap==0.1.1 | ||
| urllib3==1.24.2 # Needed by requests. | ||
| virtualenv==15.1.0 | ||
| wcwidth==0.1.7 | ||
| webencodings==0.5.1 | ||
| Werkzeug==0.15.3 # Needed by Flask. | ||
| wget==3.2 | ||
| widgetsnbextension==3.1.4 | ||
| wrapt==1.11.2 | ||
| zipp==0.6.0 # Needed by pytest. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.