diff --git a/environment/Dockerfile b/environment/Dockerfile index 33ac566..12b6039 100644 --- a/environment/Dockerfile +++ b/environment/Dockerfile @@ -9,105 +9,28 @@ ARG GIT_ACCESS_TOKEN COPY git-askpass / RUN pip install -U --no-cache-dir \ - aiobotocore==2.4.0 \ - aiohttp==3.8.3 \ - aioitertools==0.11.0 \ - aiosignal==1.3.1 \ - altair==4.2.0 \ - async-timeout==4.0.2 \ - attrs==22.1.0 \ - blinker==1.5 \ - botocore==1.27.59 \ - cachetools==5.2.0 \ - certifi \ - charset-normalizer==2.1.1 \ - click==8.1.3 \ - commonmark==0.9.1 \ - contourpy==1.0.6 \ - cycler==0.11.0 \ - decorator==5.1.1 \ - dill==0.3.6 \ - distlib==0.3.4 \ - entrypoints==0.4 \ - extra-streamlit-components==0.1.56 \ - fonttools==4.38.0 \ - frozenlist==1.3.3 \ - fsspec==2022.11.0 \ - gitdb==4.0.9 \ - GitPython==3.1.29 \ - h5py==3.8.0 \ - hdmf==3.5.2 \ - idna==3.4 \ - importlib-metadata==5.0.0 \ - Jinja2==3.1.2 \ - jmespath==1.0.1 \ - jsonschema==4.17.1 \ - kiwisolver==1.4.4 \ - MarkupSafe==2.1.1 \ - matplotlib==3.6.2 \ - multidict==6.0.2 \ - nptyping==2.4.1 \ - numpy==1.23.5 \ - packaging==21.3 \ - pandas==1.5.2 \ - patsy==0.5.3 \ - Pillow==9.3.0 \ - pipenv==2022.5.2 \ - platformdirs==2.5.2 \ - plotly==5.11.0 \ - protobuf==3.20.3 \ - psrecord==1.2 \ - psutil==5.9.4 \ - pyarrow==10.0.1 \ - pydeck==0.8.0 \ - Pygments==2.13.0 \ - pyinstrument==4.1.1 \ - Pympler==1.0.1 \ - pynrrd==1.0.0 \ - pynwb==2.3.1 \ - pyparsing==3.0.9 \ - pyrsistent==0.19.2 \ - python-dateutil==2.8.2 \ - python-decouple==3.6 \ - pytz==2022.6 \ - pytz-deprecation-shim==0.1.0.post0 \ - requests==2.31.0 \ - rich==12.6.0 \ - ruamel.yaml==0.17.21 \ - ruamel.yaml.clib==0.2.7 \ - s3fs==2022.11.0 \ - scipy==1.10.0 \ - scikit-learn==1.3.2 \ - seaborn==0.11.2 \ - six==1.16.0 \ - smmap==5.0.0 \ - statannotations==0.5.0 \ - statsmodels==0.13.5 \ streamlit==1.31.0 \ streamlit-aggrid==0.3.5 \ + streamlit-bokeh3-events==0.1.4 \ + streamlit_dynamic_filters==0.1.9 \ streamlit-nested-layout==0.1.1 \ streamlit-plotly-events==0.0.6 \ - streamlit-profiler==0.2.4 \ - tenacity==8.1.0 \ - toml==0.10.2 \ - toolz==0.12.0 \ - tornado==6.2 \ - typing_extensions==4.9.0 \ - tzdata==2022.6 \ - tzlocal==4.2 \ - urllib3==1.26.13 \ - validators==0.20.0 \ - virtualenv==20.14.1 \ - virtualenv-clone==0.5.7 \ - watchdog==2.1.9 \ - wrapt==1.14.1 \ - yarl==1.8.1 \ - zipp==3.10.0 \ - git+https://github.com/AllenNeuralDynamics/aind-foraging-behavior-bonsai-automatic-training.git@main \ pygwalker==0.4.7 \ - aind-data-access-api[docdb]==0.13.0 \ - streamlit-dynamic-filters==0.1.9 \ + extra-streamlit-components==0.1.56 \ + numpy==1.26.4 \ + pandas==2.2.2 \ + matplotlib==3.9.2 \ + seaborn==0.11.2 \ + scipy==1.13.1 \ + plotly==5.11.0 \ + statsmodels==0.13.5 \ + statannotations==0.5.0 \ + scikit-learn==1.5.1 \ semver==3.0.2 \ + s3fs==2024.6.1 \ + pillow==10.4.0 \ + aind-data-access-api[docdb]==0.13.0 \ + git+https://github.com/AllenNeuralDynamics/aind-foraging-behavior-bonsai-automatic-training.git@main \ git+https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models.git@develop \ git+https://github.com/AllenNeuralDynamics/aind-behavior-gym.git@develop diff --git a/pip_freeze.txt b/pip_freeze.txt index c4934d7..6ca262a 100644 --- a/pip_freeze.txt +++ b/pip_freeze.txt @@ -1,145 +1,248 @@ +aind-auto-train @ git+https://github.com/AllenNeuralDynamics/aind-foraging-behavior-bonsai-automatic-training.git@ad2a7f3b152f4d9f3379c01a60ffeaa23fcdcf8e +aind-behavior-gym==0.3.6 +aind-data-access-api==0.13.0 +aind-data-schema==0.38.6 +aind-data-schema-models==0.2.3 +aind-dynamic-foraging-basic-analysis==0.2.6 +aind-dynamic-foraging-models @ git+https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models.git@9f7aa0c763fa0d4fd3abf05787c36fc7addb0d30 +aind-ephys-utils==0.0.15 +aind_codeocean_api==0.5.0 aiobotocore==2.4.0 +aiofiles==22.1.0 aiohttp==3.8.3 aioitertools==0.11.0 aiosignal==1.3.1 +aiosqlite==0.18.0 altair==4.2.0 -anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1621480387968/work/dist -argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1610522574055/work -async-generator==1.10 +annotated-types==0.7.0 +anyio==3.6.2 +appdirs==1.4.4 +argon2-cffi==21.3.0 +argon2-cffi-bindings==21.2.0 +arrow==1.2.3 +asciitree==0.3.3 +astor==0.8.1 +asttokens==2.2.1 async-timeout==4.0.2 -attrs==22.1.0 -Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1619719576210/work -backcall @ file:///home/conda/feedstock_root/build_artifacts/backcall_1592338393461/work -backports.functools-lru-cache @ file:///home/conda/feedstock_root/build_artifacts/backports.functools_lru_cache_1618230623929/work -backports.zoneinfo==0.2.1 -bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1612213472466/work +attrs==24.2.0 +Babel==2.12.1 +backcall==0.2.0 +backoff==2.2.1 +bcrypt==4.2.0 +beautifulsoup4==4.11.2 +bleach==6.0.0 blinker==1.5 +bokeh==3.4.3 +boto3==1.24.59 botocore==1.27.59 brotlipy==0.7.0 cachetools==5.2.0 -certifi==2022.9.24 -cffi @ file:///tmp/build/80754af9/cffi_1605538068321/work -chardet @ file:///tmp/build/80754af9/chardet_1605303185383/work +certifi==2024.7.4 +cffi @ file:///opt/conda/conda-bld/cffi_1642701102775/work charset-normalizer==2.1.1 click==8.1.3 -colorama==0.4.4 +cloudpickle==3.0.0 +colorama @ file:///tmp/build/80754af9/colorama_1607707115595/work +comm==0.2.2 commonmark==0.9.1 -conda==4.9.2 -conda-package-handling @ file:///tmp/build/80754af9/conda-package-handling_1603018141399/work -contourpy==1.0.6 -cryptography @ file:///tmp/build/80754af9/cryptography_1605544487601/work -cycler==0.11.0 +conda==4.12.0 +conda-content-trust @ file:///tmp/build/80754af9/conda-content-trust_1617045594566/work +conda-package-handling @ file:///tmp/build/80754af9/conda-package-handling_1649105784853/work +contourpy==1.3.0 +cryptography @ file:///tmp/build/80754af9/cryptography_1639414572950/work +cycler==0.12.1 +dateutils==0.6.12 +debugpy==1.6.6 decorator==5.1.1 -defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work +defusedxml==0.7.1 +dictdiffer==0.9.0 +dill==0.3.6 +distlib==0.3.4 +dnspython==2.6.1 +docopt==0.6.2 +duckdb==0.10.0 entrypoints==0.4 +executing==1.2.0 extra-streamlit-components==0.1.56 -fonttools==4.38.0 +Farama-Notifications==0.0.4 +fasteners==0.19 +fastjsonschema==2.16.3 +filelock==3.15.4 +fonttools==4.53.1 +fqdn==1.5.1 frozenlist==1.3.3 fsspec==2022.11.0 gitdb==4.0.9 GitPython==3.1.29 -h5py==3.9.0 -hdmf==3.8.0 +graphviz==0.20.3 +greenlet==3.0.3 +gw_dsl_parser==0.1.45a6 +gymnasium==0.29.1 +h5py==3.11.0 +hdmf==3.14.3 +hdmf_zarr==0.8.0 idna==3.4 -importlib-metadata==5.0.0 -importlib-resources==6.0.0 -ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1620912944151/work/dist/ipykernel-5.5.5-py3-none-any.whl -ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1622679232122/work +importlib_metadata==8.4.0 +importlib_resources==6.4.4 +inflection==0.5.1 +ipykernel==6.21.3 +ipython==8.12.3 ipython-genutils==0.2.0 -jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1610146791023/work +ipywidgets==8.1.3 +isoduration==20.11.0 +isort==5.13.2 +jedi==0.18.2 Jinja2==3.1.2 jmespath==1.0.1 -json5 @ file:///home/conda/feedstock_root/build_artifacts/json5_1600692310011/work -jsonschema==4.17.1 -jupyter-client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1615693636836/work -jupyter-core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1612125275706/work -jupyter-packaging @ file:///home/conda/feedstock_root/build_artifacts/jupyter-packaging_1613054948399/work -jupyter-server @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_1621649383518/work -jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1614041538214/work -jupyterlab-git==0.30.0b2 -jupyterlab-pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1601375948261/work -jupyterlab-server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server_1622556871679/work -kiwisolver==1.4.4 +joblib==1.4.2 +json5==0.9.11 +jsonpointer==2.3 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +jupyter-events==0.6.3 +jupyter-ydoc==0.2.2 +jupyter_client==8.0.3 +jupyter_core==5.2.0 +jupyter_server==2.4.0 +jupyter_server_fileid==0.8.0 +jupyter_server_terminals==0.4.4 +jupyter_server_ydoc==0.6.1 +jupyterlab==3.6.1 +jupyterlab-pygments==0.2.2 +jupyterlab_server==2.20.0 +jupyterlab_widgets==3.0.11 +kanaries_track==0.0.4 +kiwisolver==1.4.5 MarkupSafe==2.1.1 -matplotlib==3.6.2 -matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1618935594181/work -mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1610112875388/work +matplotlib==3.9.2 +matplotlib-inline==0.1.6 +mistune==2.0.5 +monotonic==1.6 multidict==6.0.2 -nbclassic @ file:///home/conda/feedstock_root/build_artifacts/nbclassic_1621947328608/work -nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1614336084111/work -nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert_1605401836768/work -nbdime==2.1.0 -nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1617383142101/work -nest-asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1617163391303/work -notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1621259862661/work +nbclassic==0.5.3 +nbclient==0.7.2 +nbconvert==7.16.4 +nbformat==5.10.4 +nest-asyncio==1.5.6 +notebook==6.5.3 +notebook_shim==0.2.2 nptyping==2.4.1 -numpy==1.23.5 -packaging==21.3 -pandas==1.5.3 -pandocfilters==1.4.2 -parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1617148930513/work +numcodecs==0.12.1 +numpy==1.26.4 +packaging==24.1 +pandas==2.2.2 +pandocfilters==1.5.0 +paramiko==3.4.0 +parso==0.8.3 +pathlib==1.0.1 patsy==0.5.3 -pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1602535608087/work -pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work -Pillow==9.3.0 -pkgutil-resolve-name==1.3.10 +pexpect==4.8.0 +pickleshare==0.7.5 +pillow==10.4.0 +pipdeptree==2.23.1 +pipenv==2022.5.2 +pipreqs==0.5.0 +platformdirs==2.5.2 plotly==5.11.0 -prometheus-client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1622586138406/work -prompt-toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1616432837031/work +prometheus-client==0.16.0 +prompt-toolkit==3.0.38 protobuf==3.20.3 -ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl +psrecord==1.2 +psutil==5.9.4 +ptyprocess==0.7.0 +pure-eval==0.2.2 pyarrow==10.0.1 pycosat==0.6.3 -pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work +pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work +pydantic==2.8.2 +pydantic-settings==2.4.0 +pydantic_core==2.20.1 pydeck==0.8.0 Pygments==2.13.0 +pygwalker==0.4.7 +pyinstrument==4.1.1 +pymongo==4.3.3 Pympler==1.0.1 +PyNaCl==1.5.0 pynrrd==1.0.0 -pynwb==2.4.0 -pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1605545627475/work -pyparsing==3.0.9 +pynwb==2.8.1 +pyOpenSSL @ file:///opt/conda/conda-bld/pyopenssl_1643788558760/work +pyparsing==3.1.4 pyrsistent==0.19.2 -PySocks @ file:///tmp/build/80754af9/pysocks_1605305779399/work -python-dateutil==2.8.2 +PySocks @ file:///tmp/build/80754af9/pysocks_1605305812635/work +python-dateutil==2.9.0.post0 python-decouple==3.6 -pytz==2022.6 +python-dotenv==1.0.1 +python-json-logger==2.0.7 +pytz==2024.1 pytz-deprecation-shim==0.1.0.post0 -pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1622038460640/work -requests==2.28.1 +PyYAML==6.0 +pyzmq==25.0.0 +referencing==0.35.1 +requests==2.31.0 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 rich==12.6.0 -ruamel-yaml==0.15.87 -ruamel.yaml.clib==0.2.7 +rpds-py==0.20.0 +ruamel-yaml-conda @ file:///tmp/build/80754af9/ruamel_yaml_1616016711199/work +ruamel.yaml==0.18.6 +ruamel.yaml.clib==0.2.8 s3fs==2022.11.0 -scipy==1.10.0 -seaborn==0.12.2 -semver==2.13.0 -Send2Trash==1.5.0 +s3transfer==0.6.2 +scikit-learn==1.5.1 +scipy==1.13.1 +seaborn==0.11.2 +segment-analytics-python==2.2.3 +semver==3.0.2 +Send2Trash==1.8.0 six==1.16.0 smmap==5.0.0 -sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1610318319305/work +sniffio==1.3.0 +soupsieve==2.4 +SQLAlchemy==2.0.32 +sqlglot==25.10.0 +sshtunnel==0.4.0 +stack-data==0.6.2 statannotations==0.5.0 -statsmodels==0.14.0 -streamlit==1.19.0 -streamlit-aggrid==0.3.3 +statsmodels==0.13.5 +streamlit==1.31.0 +streamlit-aggrid==0.3.5 +streamlit-bokeh3-events==0.1.4 streamlit-nested-layout==0.1.1 streamlit-plotly-events==0.0.6 +streamlit-profiler==0.2.4 +streamlit_dynamic_filters==0.1.9 tenacity==8.1.0 -terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1621535185113/work -testpath @ file:///home/conda/feedstock_root/build_artifacts/testpath_1621261527237/work +terminado==0.17.1 +threadpoolctl==3.5.0 +tinycss2==1.2.1 toml==0.10.2 +tomli==2.0.1 toolz==0.12.0 tornado==6.2 -tqdm @ file:///tmp/build/80754af9/tqdm_1605303662894/work -traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1602771532708/work -typing-extensions==4.4.0 -tzdata==2022.6 +tqdm @ file:///opt/conda/conda-bld/tqdm_1647339053476/work +traitlets==5.9.0 +typing_extensions==4.12.2 +tzdata==2024.1 tzlocal==4.2 +uri-template==1.2.0 urllib3==1.26.13 validators==0.20.0 +virtualenv==20.14.1 +virtualenv-clone==0.5.7 +wasmtime==12.0.0 watchdog==2.1.9 -wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1600965781394/work +wcwidth==0.2.6 +webcolors==1.12 webencodings==0.5.1 -websocket-client @ file:///home/conda/feedstock_root/build_artifacts/websocket-client_1610127644879/work +websocket-client==1.5.1 +widgetsnbextension==4.0.11 wrapt==1.14.1 +xarray==2024.7.0 +xyzservices==2024.6.0 +y-py==0.5.9 +yarg==0.1.9 yarl==1.8.1 -zipp==3.10.0 +ypy-websocket==0.8.2 +zarr==2.18.2 +zipp==3.20.1 diff --git a/requirements.txt b/requirements.txt index 6573052..edcd49f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,101 +1,24 @@ -aiobotocore==2.4.0 -aiohttp==3.8.3 -aioitertools==0.11.0 -aiosignal==1.3.1 -altair==4.2.0 -async-timeout==4.0.2 -attrs==22.1.0 -blinker==1.5 -botocore==1.27.59 -cachetools==5.2.0 -certifi -charset-normalizer==2.1.1 -click==8.1.3 -commonmark==0.9.1 -contourpy==1.0.6 -cycler==0.11.0 -decorator==5.1.1 -dill==0.3.6 -distlib==0.3.4 -entrypoints==0.4 -extra-streamlit-components==0.1.56 -fonttools==4.38.0 -frozenlist==1.3.3 -fsspec==2022.11.0 -gitdb==4.0.9 -GitPython==3.1.29 -h5py==3.8.0 -hdmf==3.5.2 -idna==3.4 -importlib-metadata==5.0.0 -Jinja2==3.1.2 -jmespath==1.0.1 -jsonschema==4.17.1 -kiwisolver==1.4.4 -MarkupSafe==2.1.1 -matplotlib==3.6.2 -multidict==6.0.2 -nptyping==2.4.1 -numpy==1.23.5 -packaging==21.3 -pandas==1.5.2 -patsy==0.5.3 -Pillow==9.3.0 -pipenv==2022.5.2 -platformdirs==2.5.2 -plotly==5.11.0 -protobuf==3.20.3 -psrecord==1.2 -psutil==5.9.4 -pyarrow==10.0.1 -pydeck==0.8.0 -Pygments==2.13.0 -pyinstrument==4.1.1 -Pympler==1.0.1 -pynrrd==1.0.0 -pynwb==2.3.1 -pyparsing==3.0.9 -pyrsistent==0.19.2 -python-dateutil==2.8.2 -python-decouple==3.6 -pytz==2022.6 -pytz-deprecation-shim==0.1.0.post0 -requests==2.31.0 -rich==12.6.0 -ruamel.yaml==0.17.21 -ruamel.yaml.clib==0.2.7 -s3fs==2022.11.0 -scipy==1.10.0 -scikit-learn==1.3.2 -seaborn==0.11.2 -six==1.16.0 -smmap==5.0.0 -statannotations==0.5.0 -statsmodels==0.13.5 streamlit==1.31.0 streamlit-aggrid==0.3.5 +streamlit-bokeh3-events==0.1.4 +streamlit_dynamic_filters==0.1.9 streamlit-nested-layout==0.1.1 streamlit-plotly-events==0.0.6 -streamlit-profiler==0.2.4 -tenacity==8.1.0 -toml==0.10.2 -toolz==0.12.0 -tornado==6.2 -typing_extensions==4.9.0 -tzdata==2022.6 -tzlocal==4.2 -urllib3==1.26.13 -validators==0.20.0 -virtualenv==20.14.1 -virtualenv-clone==0.5.7 -watchdog==2.1.9 -wrapt==1.14.1 -yarl==1.8.1 -zipp==3.10.0 -git+https://github.com/AllenNeuralDynamics/aind-foraging-behavior-bonsai-automatic-training.git@main pygwalker==0.4.7 -aind-data-access-api[docdb]==0.13.0 -streamlit-dynamic-filters==0.1.9 +extra-streamlit-components==0.1.56 +numpy==1.26.4 +pandas==2.2.2 +matplotlib==3.9.2 +seaborn==0.11.2 +scipy==1.13.1 +plotly==5.11.0 +statsmodels==0.13.5 +statannotations==0.5.0 +scikit-learn==1.5.1 semver==3.0.2 +s3fs==2024.6.1 +pillow==10.4.0 +aind-data-access-api[docdb]==0.13.0 +git+https://github.com/AllenNeuralDynamics/aind-foraging-behavior-bonsai-automatic-training.git@main git+https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models.git@develop -git+https://github.com/AllenNeuralDynamics/aind-behavior-gym.git@develop +git+https://github.com/AllenNeuralDynamics/aind-behavior-gym.git@develop \ No newline at end of file