diff --git a/conda/Makefile b/conda/Makefile index a6089e4..56fc3b1 100644 --- a/conda/Makefile +++ b/conda/Makefile @@ -4,13 +4,6 @@ NAME = deepali # Relative path of repository root directory ROOT = .. -# Commands -CONDA = mamba -CONDA_OPTS = --no-banner -CONDA_DEVENV = conda devenv -CONDA_LOCK = conda-lock -CONDA_LOCK_OPTS = --mamba - # Name of conda-devenv configuration file DEVENV = environment.devenv.yml @@ -66,20 +59,20 @@ clear: @rm -f $(LOCKFILE) environment.devenv.{linux-64,osx-64,win-64}.yml environment.{linux-64,osx-64,win-64}.{lock,yml} lock-linux: - @$(CONDA_DEVENV) --name $(NAME) --file $(DEVENV) --env-manager $(CONDA) --env-var PLATFORM=linux-64 --print > environment.devenv.linux-64.yml - @$(CONDA_LOCK) $(CONDA_LOCK_OPTS) --lockfile $(LOCKFILE) --platform linux-64 --file environment.devenv.linux-64.yml + conda devenv --name $(NAME) --file $(DEVENV) --env-manager conda --env-var PLATFORM=linux-64 --print > environment.devenv.linux-64.yml + conda lock --lockfile $(LOCKFILE) --platform linux-64 --file environment.devenv.linux-64.yml lock-osx: - @$(CONDA_DEVENV) --name $(NAME) --file $(DEVENV) --env-manager $(CONDA) --env-var PLATFORM=osx-64 --print > environment.devenv.osx-64.yml - @$(CONDA_LOCK) $(CONDA_LOCK_OPTS) --lockfile $(LOCKFILE) --platform osx-64 --file environment.devenv.osx-64.yml + conda devenv --name $(NAME) --file $(DEVENV) --env-manager conda --env-var PLATFORM=osx-64 --print > environment.devenv.osx-64.yml + conda lock --lockfile $(LOCKFILE) --platform osx-64 --file environment.devenv.osx-64.yml lock-win: - @$(CONDA_DEVENV) --name $(NAME) --file $(DEVENV) --env-manager $(CONDA) --env-var PLATFORM=win-64 --print > environment.devenv.win-64.yml - @$(CONDA_LOCK) $(CONDA_LOCK_OPTS) --lockfile $(LOCKFILE) --platform win-64 --file environment.devenv.win-64.yml + conda devenv --name $(NAME) --file $(DEVENV) --env-manager conda --env-var PLATFORM=win-64 --print > environment.devenv.win-64.yml + conda lock --lockfile $(LOCKFILE) --platform win-64 --file environment.devenv.win-64.yml render: - @$(CONDA_LOCK) render $(LOCKFILE) --kind env --filename-template environment.{platform} - @$(CONDA_LOCK) render $(LOCKFILE) --kind explicit --filename-template environment.{platform}.lock + conda lock render $(LOCKFILE) --kind env --filename-template environment.{platform} + conda lock render $(LOCKFILE) --kind explicit --filename-template environment.{platform}.lock @if ! grep -e 'pytorch.*cuda' environment.linux-64.lock > /dev/null 2> /dev/null; then \ echo "Expected PyTorch with CUDA support for PLATFORM=linux-64. Check conda configuration."; \ fi @@ -88,10 +81,10 @@ render: env: create-env install create-env: - @$(CONDA) $(CONDA_OPTS) create --name $(NAME) --file environment.$(PLATFORM).lock + conda create --name $(NAME) --file environment.$(PLATFORM).lock update-env: - @$(CONDA) $(CONDA_OPTS) update --name $(NAME) --file environment.$(PLATFORM).lock --prune + conda update --name $(NAME) --file environment.$(PLATFORM).lock --prune install: - @$(CONDA) $(CONDA_OPTS) run --name $(NAME) pip install $(PIP_INSTALL_OPTS) ./$(ROOT)[utils] + conda run --name $(NAME) pip install $(PIP_INSTALL_OPTS) ./$(ROOT)[utils] diff --git a/conda/README.md b/conda/README.md index f551199..4ebaf52 100644 --- a/conda/README.md +++ b/conda/README.md @@ -5,7 +5,7 @@ Conda environment configurations for `deepali` libraries. ## Create environment -If not done before, install either [Miniconda](https://docs.conda.io/en/latest/miniconda.html) or [Anaconda](https://www.anaconda.com/). +If not done before, install either [Anaconda], [Miniconda], or [Mambaforge]. A conda environment for this project can be created using the `env` Makefile target, i.e., @@ -22,7 +22,7 @@ NAME=deepali PLATFORM=linux-64 conda create --name $NAME --file environment.$PLATFORM.lock -conda run --name $NAME pip install [--editable] .. +conda run --name $NAME pip install ..[utils] ``` where `PLATFORM` is one of the following values. @@ -38,16 +38,21 @@ where `PLATFORM` is one of the following values. The following tools are required to update the generated dependency files. -1. Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html): Package dependency management tool. -2. Install [mamba](https://mamba.readthedocs.io/en/latest/): Faster dependency resolution and more informative error messages. - - `conda install mamba=0.23 --name base --channel conda-forge` -3. Install [conda-devenv](https://conda-devenv.readthedocs.io/en/latest/): Advanced conda environment configuration such as conditional dependencies. - - `conda install conda-devenv=2.3 --name base --channel conda-forge` -4. Install [conda-lock](https://conda-incubator.github.io/conda-lock/): Lock versions of dependencies and generate explicit lockfiles. - - `conda install conda-lock=1.0 --name base --channel conda-forge` +1. Install [Mambaforge]: Package dependency management tool. +3. Install [conda-devenv]: Advanced conda environment configuration such as conditional dependencies. + - `mamba --no-banner install conda-devenv=2.3 --name base --channel conda-forge` +4. Install [conda-lock]: Lock versions of dependencies and generate explicit lockfiles. + - `mamba --no-banner install conda-lock=1.0 --name base --channel conda-forge` After editing the `environment.devenv.yml` file to add, remove, or update required and optional dependencies, run the following command to re-generate the `environment.conda-lock.yml` and `environment.*.lock` files. ``` make all ``` + + +[Anaconda]: https://www.anaconda.com/ +[Mambaforge]: https://mamba.readthedocs.io/en/latest/installation.html +[Miniconda]: https://docs.conda.io/en/latest/miniconda.html +[conda-devenv]: https://conda-devenv.readthedocs.io/en/latest/ +[conda-lock]: https://conda-incubator.github.io/conda-lock/ diff --git a/conda/environment.conda-lock.yml b/conda/environment.conda-lock.yml index 8b35dbc..8c526f0 100644 --- a/conda/environment.conda-lock.yml +++ b/conda/environment.conda-lock.yml @@ -21,9 +21,9 @@ metadata: - url: nodefaults used_env_vars: [] content_hash: - linux-64: c6bd68ba63788a00937c8cd1d91bb1e5813d242d7089005156ab1a663f53aee1 - osx-64: 533a7567b393584157366e71374225596e814fe74cfcb03642d3b4e184d58c87 - win-64: 6255d416b6866feefaa84cbaf27b3a7608f8bb60e8d5e51ca00574e0f3970f20 + linux-64: 586016f05a089668afa3f0a057304e5826b41e87317e8d51969529896659d6a0 + osx-64: 1e6e6cea02ff8fd576a8852899876561e48ebb709abcd877d8d931d3b50338da + win-64: f9e524a368611b4591c0b79cc851d7fd034bcb935240ad118e3fe4c7b27edeb4 platforms: - linux-64 - osx-64 @@ -47,14 +47,14 @@ package: - category: main dependencies: {} hash: - md5: f5c65075fc34438d5b456c7f3f5ab695 - sha256: 0cf1bb3d0bfc5519b60af2c360fa4888fb838e1476b1e0f65b9dbc48b45c7345 + md5: a73ecd2988327ad4c8f2c331482917f2 + sha256: 525b7b6b5135b952ec1808de84e5eca57c7c7ff144e29ef3e96ae4040ff432c1 manager: conda name: ca-certificates optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda - version: 2023.5.7 + url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda + version: 2023.7.22 - category: main dependencies: {} hash: @@ -463,14 +463,14 @@ package: libgcc-ng: '>=12' libstdcxx-ng: '>=12' hash: - md5: c2acfc9bc0d0c53f83bbf0f582cb0e7a - sha256: 1dfe42f82ccd06ca4b19cfbbef483385f284be90f6b40c26831004b192c98bda + md5: b1b879d6d093f55dd40d58b5eb2f0699 + sha256: 53b15a98aadbe0704479bacaf7a5618fcb32d1577be320630674574241639b34 manager: conda name: eigen optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.1-h00ab1b0_0.conda - version: 3.4.1 + url: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda + version: 3.4.0 - category: main dependencies: libgcc-ng: '>=12' @@ -1015,14 +1015,14 @@ package: ca-certificates: '' libgcc-ng: '>=12' hash: - md5: 2e1d7b458ac8f1e3ca4e18b77add6277 - sha256: 407d655643389bdb49266842a816815c981ae98f3513a6a2059b908b3abb380a + md5: e5ac5227582d6c83ccf247288c0eb095 + sha256: b113fbac327c90cdc29c2fac0f2a2e5cc0d1918b2a5ffa7abd49b695b9b3c6e9 manager: conda name: openssl optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.1-hd590300_1.conda - version: 3.1.1 + url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda + version: 3.1.2 - category: main dependencies: libgcc-ng: '>=7.5.0' @@ -2159,6 +2159,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.13-pyhd8ed1ab_0.conda version: 0.7.13 +- category: main + dependencies: + python: '' + hash: + md5: 5f095bc6454094e96f146491fd03633b + sha256: ae9fb8f68281f84482f2c234379aa12405a9e365151d43af20b3ae1f17312111 + manager: conda + name: appdirs + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2 + version: 1.4.4 - category: main dependencies: libgcc-ng: '>=12' @@ -2221,6 +2233,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/blinker-1.6.2-pyhd8ed1ab_0.conda version: 1.6.2 +- category: main + dependencies: + python: 2.7.*|>=3.7 + hash: + md5: 033eb25fffd222aceeca6d58cd953680 + sha256: 4ff828cceb8f55cb26d23b1a4c174d22c7cd92350221724bcaf2d6632e33fdee + manager: conda + name: boltons + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/boltons-23.0.0-pyhd8ed1ab_0.conda + version: 23.0.0 - category: main dependencies: brotli-bin: 1.0.9 h166bdaf_9 @@ -2236,6 +2260,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.0.9-h166bdaf_9.conda version: 1.0.9 +- category: main + dependencies: + python: '>=3.6' + hash: + md5: 576d629e47797577ab0f1b351297ef4a + sha256: 6dbf7a5070cc43d90a1e4c2ec0c541c69d8e30a0e25f50ce9f6e4a432e42c5d7 + manager: conda + name: cached_property + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2 + version: 1.5.2 - category: main dependencies: python: '>=3.7' @@ -2252,14 +2288,14 @@ package: dependencies: python: '>=3.7' hash: - md5: 5d1b71c942b8421285934dad1d891ebc - sha256: f839a6e04d94069f90dd85337ea9108f058dc76771bb469a413f32bb1ba0b256 + md5: 7f3dbc9179b4dde7da98dfb151d0ad22 + sha256: db66e31866ff4250c190788769e3a8a1709237c3e9c38d7143aae95ab75fcb31 manager: conda name: certifi optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/noarch/certifi-2023.5.7-pyhd8ed1ab_0.conda - version: 2023.5.7 + url: https://conda.anaconda.org/conda-forge/noarch/certifi-2023.7.22-pyhd8ed1ab_0.conda + version: 2023.7.22 - category: main dependencies: python: '>=3.7' @@ -2297,6 +2333,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2 version: 0.4.6 +- category: main + dependencies: + python: '>=3.6,<4.0' + hash: + md5: 709a2295dd907bb34afb57d54320642f + sha256: 2f05954a3faf0700c14c1deddc085385160ee32abe111699c78d9cb277e915cc + manager: conda + name: crashtest + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/crashtest-0.4.1-pyhd8ed1ab_0.tar.bz2 + version: 0.4.1 - category: main dependencies: python: '>=3.6' @@ -2342,14 +2390,14 @@ package: python: '>=3.10,<3.11.0a0' python_abi: 3.10.* *_cp310 hash: - md5: 8ffb020d2b722c962f0b4f06a304f533 - sha256: 4e476f11daa93d7740eaa8b13238db48c8c9e416d127bb1cda30300b63a26b52 + md5: 397d3d6153c0b8de807e1bdc58b16013 + sha256: da916d36136e7e756964d7e9d68ab6f1012f3d0f6fe0a57783863a4bf66819f4 manager: conda name: debugpy optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.6.7-py310heca2aa9_0.conda - version: 1.6.7 + url: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.6.8-py310hc6cd4ac_0.conda + version: 1.6.8 - category: main dependencies: python: '>=3.5' @@ -2374,6 +2422,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2 version: 0.7.1 +- category: main + dependencies: + python: 2.7|>=3.6 + hash: + md5: 12d8aae6994f342618443a8f05c652a0 + sha256: 13c887cb4a29e1e853a118cfc0e42b72a7e1d1c50c66c0974885d37f0db30619 + manager: conda + name: distlib + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.7-pyhd8ed1ab_0.conda + version: 0.3.7 - category: main dependencies: python: '>=3.10,<3.11.0a0' @@ -2633,6 +2693,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-py_1.tar.bz2 version: 0.2.0 +- category: main + dependencies: + python: '>=3.7' + hash: + md5: 9800ad1699b42612478755a2d26c722d + sha256: 16639759b811866d63315fe1391f6fb45f5478b823972f4d3d9f0392b7dd80b8 + manager: conda + name: jeepney + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/jeepney-0.8.0-pyhd8ed1ab_0.tar.bz2 + version: 0.8.0 - category: main dependencies: python: '>=3.7' @@ -2645,6 +2717,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/jmespath-1.0.1-pyhd8ed1ab_0.tar.bz2 version: 1.0.1 +- category: main + dependencies: + python: '' + hash: + md5: 07d85c22a3beb102a48cd123df84c2a6 + sha256: da279af2285d8f575a7f5652e83bf7f36155c4c63154e385a9d171efcc607bc1 + manager: conda + name: jsonpointer + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/jsonpointer-2.0-py_0.tar.bz2 + version: '2.0' - category: main dependencies: python: '>=3.7' @@ -2707,13 +2791,13 @@ package: libstdcxx-ng: '>=12' libzlib: '>=1.2.13,<1.3.0a0' hash: - md5: 907344cee64101d44d806bbe0fccb01d - sha256: d9f9fb5622489d7e5c3237a4a6a46db20ead3c6bafb7277de1a25278db59b863 + md5: 1720df000b48e31842500323cb7be18c + sha256: df1221a9a05b9bb3bd9b43c08a7e2fe57a0e15a0010ef26065f7ed7666083f45 manager: conda name: libclang13 optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_h9986a30_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_h9986a30_3.conda version: 15.0.7 - category: main dependencies: @@ -2798,6 +2882,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/libwebp-1.2.4-h522a892_0.tar.bz2 version: 1.2.4 +- category: main + dependencies: + python: '' + hash: + md5: c104d98e09c47519950cffb8dd5b4f10 + sha256: d3a68045ef74a2a7b8c8a55b242fdbc875d362e37adcf793613cf0d8c8e4fbf7 + manager: conda + name: lockfile + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/lockfile-0.12.2-py_1.tar.bz2 + version: 0.12.2 - category: main dependencies: python: '>=3.10,<3.11.0a0' @@ -2861,6 +2957,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/mistune-3.0.0-pyhd8ed1ab_0.conda version: 3.0.0 +- category: main + dependencies: + python: '>=3.8' + hash: + md5: 8549fafed0351bbfaa1ddaa15fdf9b4e + sha256: 07ce65497dec537e490992758934ddbc4fb5ed9285b41387a7cca966f1a98a0f + manager: conda + name: more-itertools + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.1.0-pyhd8ed1ab_0.conda + version: 10.1.0 - category: main dependencies: python: '>=3.6' @@ -2873,6 +2981,21 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/mpmath-1.3.0-pyhd8ed1ab_0.conda version: 1.3.0 +- category: main + dependencies: + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' + python: '>=3.10,<3.11.0a0' + python_abi: 3.10.* *_cp310 + hash: + md5: 5311a49aaea44b73935c84a6d9a68e5f + sha256: da5030f22f6d1293ccdefefde17fcf1a5f337f87179c54dee2a2a1fc16d6d73a + manager: conda + name: msgpack-python + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/msgpack-python-1.0.5-py310hdf3cbec_0.conda + version: 1.0.5 - category: main dependencies: libgcc-ng: '>=12' @@ -2991,14 +3114,14 @@ package: dependencies: python: '>=3.7' hash: - md5: dbb80d1e8dc2dba5c8b106dc0768ad45 - sha256: d94463e0a140ead5c01990b565a1a21b85cb3831d56fed5955b5446bd5df33fe + md5: e41debb259e68490e3ab81e46b639ab6 + sha256: 7bcfa6d86359d45572ba9ccaeaedc04b0452e2654fe44b6fe378d0d37b8745e1 manager: conda name: pathspec optional: false platform: linux-64 - url: https://conda.anaconda.org/conda-forge/noarch/pathspec-0.11.1-pyhd8ed1ab_0.conda - version: 0.11.1 + url: https://conda.anaconda.org/conda-forge/noarch/pathspec-0.11.2-pyhd8ed1ab_0.conda + version: 0.11.2 - category: main dependencies: python: '>=3' @@ -3011,6 +3134,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2 version: 0.7.5 +- category: main + dependencies: + python: '>=3.6' + hash: + md5: 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- url: https://conda.anaconda.org/conda-forge/win-64/pyqt-5.15.7-py310h1fd54f2_3.conda - version: 5.15.7 + url: https://conda.anaconda.org/conda-forge/win-64/pyqt-5.15.9-py310h1fd54f2_4.conda + version: 5.15.9 +- category: main + dependencies: + numpy: '' + python: '>=3.10,<3.11.0a0' + python_abi: 3.10.* *_cp310 + ucrt: '>=10.0.20348.0' + vc: '>=14.2,<15' + vs2015_runtime: '>=14.29.30139' + hash: + md5: 7e623c5592d080ea8211f94e3755ee76 + sha256: 648ab3a1c42a8ce056c4ab11bd36f6d8023f9a124360b9c43037e87bcf78b704 + manager: conda + name: rapidfuzz + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/win-64/rapidfuzz-2.15.1-py310h00ffb61_0.conda + version: 2.15.1 - category: main dependencies: oauthlib: '>=3.0.0' @@ -17589,6 +19768,19 @@ package: platform: win-64 url: https://conda.anaconda.org/conda-forge/noarch/requests-oauthlib-1.3.1-pyhd8ed1ab_0.tar.bz2 version: 1.3.1 +- category: main + dependencies: + python: '>=3.6' + requests: '>=2.0.1,<3.0.0' + hash: + md5: 99c98318c8646b08cc764f90ce98906e + sha256: 20eaefc5dba74ff6c31e537533dde59b5b20f69e74df49dff19d43be59785fa3 + manager: conda + name: requests-toolbelt + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/noarch/requests-toolbelt-1.0.0-pyhd8ed1ab_0.conda + version: 1.0.0 - category: main dependencies: botocore: '>=1.12.36,<2.0a.0' @@ -17711,6 +19903,50 @@ package: platform: win-64 url: https://conda.anaconda.org/conda-forge/noarch/boto3-1.26.165-pyhd8ed1ab_0.conda version: 1.26.165 +- category: main + dependencies: + cachecontrol: 0.12.14 pyhd8ed1ab_0 + lockfile: '>=0.9' + python: '>=3.6' + hash: + md5: 43ed0c094b39bb352382db8105ab0b94 + sha256: 23af777f65d74f18aaee1641add3b15bd442096f9c4940270151704f1aa38198 + manager: conda + name: cachecontrol-with-filecache + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/noarch/cachecontrol-with-filecache-0.12.14-pyhd8ed1ab_0.conda + version: 0.12.14 +- category: main + dependencies: + crashtest: '>=0.4.1,<0.5.0' + python: '>=3.7,<4.0' + rapidfuzz: '>=2.2.0,<3.0.0' + hash: + md5: f1c5f2af6676cbe9206e191d1e70f661 + sha256: cf9bc4c9356ad8eb68512446eebc076386f2bfb8ca86626e8796621bc5a13082 + manager: conda + name: cleo + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/noarch/cleo-2.0.1-pyhd8ed1ab_0.conda + version: 2.0.1 +- category: main + dependencies: + conda: '>=4.3' + jinja2: '' + packaging: '' + python: '>=3.6' + pyyaml: '' + hash: + md5: 9b175e69c1c601d01ab5edccf822363c + sha256: 3244e025f3d185f56fb44a44d02526797ce3e95302a868867af6dc9e2e55ebe3 + manager: conda + name: conda-devenv + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/noarch/conda-devenv-2.3.0-pyhd8ed1ab_0.tar.bz2 + version: 2.3.0 - category: main dependencies: click: '>=6.0.0' @@ -17726,23 +19962,6 @@ package: platform: win-64 url: https://conda.anaconda.org/conda-forge/noarch/google-auth-oauthlib-1.0.0-pyhd8ed1ab_1.conda version: 1.0.0 -- category: main - dependencies: - ipykernel: '>=4.5.1' - ipython: '>=6.1.0' - jupyterlab_widgets: '>=3.0.7,<3.1.0' - python: '>=3.7' - traitlets: '>=4.3.1' - widgetsnbextension: '>=4.0.7,<4.1.0' - hash: - md5: 4b0f4e8fe2a303e472674eae0340bdad - sha256: 3b17ad90294f0684fca9191f1e696e9b4f03a652d5e588b6ff0feb5647fcf116 - manager: conda - name: ipywidgets - optional: false - platform: win-64 - url: https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.7-pyhd8ed1ab_0.conda - version: 8.0.7 - category: main dependencies: ipykernel: '>=6.14' @@ -17841,18 +20060,18 @@ package: version: 0.18.1 - category: main dependencies: - nbconvert-core: 7.7.1 pyhd8ed1ab_1 + nbconvert-core: 7.7.3 pyhd8ed1ab_0 pandoc: '' python: '>=3.8' hash: - md5: 796b056965d7146bcac082fa2a83943d - sha256: b5b2823e7951a5ba41b1020b7cce109fec7f2ebe540234bf8a17c54615c2f679 + md5: f44109e52a40b8149156f5ddd9c11b26 + sha256: c9fceb914dd4a8fe64b1403a0c7b0c69b5c67fc726aa8239e5ecb450d27e6963 manager: conda name: nbconvert-pandoc optional: false platform: win-64 - url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.7.1-pyhd8ed1ab_1.conda - version: 7.7.1 + url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.7.3-pyhd8ed1ab_0.conda + version: 7.7.3 - category: main dependencies: accessible-pygments: '' @@ -18135,18 +20354,18 @@ package: version: 0.17.2 - category: main dependencies: - nbconvert-core: 7.7.1 pyhd8ed1ab_1 - nbconvert-pandoc: 7.7.1 pyhd8ed1ab_1 + nbconvert-core: 7.7.3 pyhd8ed1ab_0 + nbconvert-pandoc: 7.7.3 pyhd8ed1ab_0 python: '>=3.8' hash: - md5: 95d9d1523df069792cd059f412be0d6e - sha256: c49a87861db316b322f919825820bc7193cbfa8a4a8b21b5ffe16a133644d400 + md5: f53d92ecd7d8563b006107f6a33e55c6 + sha256: 2b9e7bc41ee0882d7829e984cb1a18f039a5f756b5b747f6a3ce352bc72e5103 manager: conda name: nbconvert optional: false platform: win-64 - url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.7.1-pyhd8ed1ab_1.conda - version: 7.7.1 + url: https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.7.3-pyhd8ed1ab_0.conda + version: 7.7.3 - category: main dependencies: jupyter_server: '>=1.8,<3' @@ -18160,6 +20379,47 @@ package: platform: win-64 url: https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.3-pyhd8ed1ab_0.conda version: 0.2.3 +- category: main + dependencies: + __win: '' + backports.cached-property: '>=1.0.2,<2.0.0' + cachecontrol-with-filecache: '>=0.12.9,<0.13.0' + cleo: '>=2.0.0,<3.0.0' + crashtest: '>=0.4.1,<0.5.0' + dulwich: '>=0.21.2,<0.22.0' + filelock: '>=3.8.0,<4.0.0' + html5lib: '>=1.0.0,<2.0.0' + importlib-metadata: '>=4.4' + jsonschema: '>=4.10.0,<5.0.0' + keyring: '>=23.9.0,<24.0.0' + lockfile: '>=0.12.2,<0.13.0' + packaging: '>=20.4' + pexpect: '>=4.7.0,<5.0.0' + pkginfo: '>=1.9.4,<2.0' + platformdirs: '>=3.0.0,<4.0.0' + poetry-core: 1.6.1.* + poetry-plugin-export: '>=1.4.0,<2.0.0' + pyproject_hooks: '>=1.0.0,<2.0.0' + python: '>=3.7.0,<4.0.0' + python-build: '>=0.10.0,<0.11.0' + python-installer: '>=0.7.0,<0.8.0' + requests: '>=2.18,<3.0' + requests-toolbelt: '>=0.9.1,<2' + shellingham: '>=1.5.0,<2.0.0' + tomli: '>=2.0.1,<3.0.0' + tomlkit: '>=0.11.4,<1.0.0' + trove-classifiers: '>=2022.5.19' + urllib3: '>=1.26.0,<2.0.0' + virtualenv: '>=20.22.0,<21.0.0' + hash: + md5: 278a253d341cdb93af47a14c794f6c02 + sha256: 03eee33329dceb0b2a5d88eac3bff5a316bf75046f4634b53d1e6816588325a8 + manager: conda + name: poetry + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/noarch/poetry-1.5.1-win_pyhd8ed1ab_0.conda + version: 1.5.1 - category: main dependencies: blas: '* mkl' @@ -18270,6 +20530,30 @@ package: platform: win-64 url: https://conda.anaconda.org/conda-forge/noarch/tensorboard-2.13.0-pyhd8ed1ab_0.conda version: 2.13.0 +- category: main + dependencies: + click: '>=8.0' + click-default-group: '' + ensureconda: '>=1.3' + jinja2: '' + poetry: '' + pydantic: '>=1.8.1' + python: '>=3.6' + pyyaml: '>=5.1' + requests: '>=2' + ruamel.yaml: '' + setuptools: '' + toml: '' + typing-extensions: '' + hash: + md5: 1c31d380288fc1599fb5f4c76c8c828c + sha256: 2895546468293f358395b072846ebf8a2e04339d1355009fb96787d804250bb0 + manager: conda + name: conda-lock + optional: false + platform: win-64 + url: https://conda.anaconda.org/conda-forge/noarch/conda-lock-1.0.5-pyhd8ed1ab_1.tar.bz2 + version: 1.0.5 - category: main dependencies: click: '>=7.1,<9' @@ -18419,14 +20703,14 @@ package: tqdm: '>=4.57.0' typing_extensions: '>=4.0.0' hash: - md5: ce9d626b181c6f8cceb5047f6a819f7d - sha256: a049296b4b33bceedf3bafd378e8a4112bca71b453734f1e0daaca2a72598593 + md5: 5325b6adf171d4d69968100af806994e + sha256: 54efb4be9a8f73692cf24f85923a226c0ed6d035000704479b0f27288bb0a874 manager: conda name: pytorch-lightning optional: false platform: win-64 - url: https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.0.4-pyhd8ed1ab_0.conda - version: 2.0.4 + url: https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.0.6-pyhd8ed1ab_0.conda + version: 2.0.6 - category: main dependencies: ipykernel: '' diff --git a/conda/environment.devenv.yml b/conda/environment.devenv.yml index 6966d8a..387cc3e 100644 --- a/conda/environment.devenv.yml +++ b/conda/environment.devenv.yml @@ -12,6 +12,8 @@ dependencies: - setuptools-scm =7.1 # Developer tools - black =22.3 + - conda-devenv=2.3 + - conda-lock=1.0 - docutils =0.17 - flake8 =6.0 - flake8-black =0.3.6 @@ -39,7 +41,6 @@ dependencies: - pytorch =2.0,!=2.0.0 # ["osx" not in get_env("PLATFORM")] - pytorch-cuda =11.8 # ["osx" not in get_env("PLATFORM")] - pytorch::pytorch =2.0,!=2.0.0 # ["osx" in get_env("PLATFORM")] - - pyyaml =6.0 - ruamel.yaml =0.17 - SimpleITK =2.2 # Utility libraries diff --git a/conda/environment.linux-64.lock b/conda/environment.linux-64.lock index f014333..d597ce6 100644 --- a/conda/environment.linux-64.lock +++ b/conda/environment.linux-64.lock @@ -1,9 +1,9 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: c6bd68ba63788a00937c8cd1d91bb1e5813d242d7089005156ab1a663f53aee1 +# input_hash: 586016f05a089668afa3f0a057304e5826b41e87317e8d51969529896659d6a0 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda#f5c65075fc34438d5b456c7f3f5ab695 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2 https://conda.anaconda.org/nvidia/linux-64/cuda-cudart-11.8.89-0.tar.bz2#b68c7ef3eda01e95d5903fb508c5e440 https://conda.anaconda.org/nvidia/linux-64/cuda-cupti-11.8.87-0.tar.bz2#2f4b4933285400137cf029fef9a7daa6 https://conda.anaconda.org/nvidia/linux-64/cuda-nvrtc-11.8.89-0.tar.bz2#f4af75ee32661708c979630cdb8f4987 @@ -39,7 +39,7 @@ https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2#d9 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda#e8c18d865be43e2fb3f7a145b6adf1f5 https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.2.0-h27087fc_1.tar.bz2#5a7e0df95874e7ffe8b7840907058563 -https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.1-h00ab1b0_0.conda#c2acfc9bc0d0c53f83bbf0f582cb0e7a +https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda#b1b879d6d093f55dd40d58b5eb2f0699 https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hc118613_108.conda#6fa90698000b05dfe8ce6515794fe71a https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2#14947d8770185e5153fdd04d4673ed37 @@ -83,7 +83,7 @@ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681 https://conda.anaconda.org/conda-forge/linux-64/nettle-3.8.1-hc379101_1.tar.bz2#3cb2c7df59990bd37c2ce27fd906de68 https://conda.anaconda.org/conda-forge/linux-64/nspr-4.35-h27087fc_0.conda#da0ec11a6454ae19bff5b02ed881a2b1 https://conda.anaconda.org/conda-forge/linux-64/openh264-2.3.1-hcb278e6_2.conda#37d01894f256b2a6921c5a218f42f8a2 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.1-hd590300_1.conda#2e1d7b458ac8f1e3ca4e18b77add6277 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda#e5ac5227582d6c83ccf247288c0eb095 https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2#660e72c82f2e75a6b3fe6a6e75c79f19 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036 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https://conda.anaconda.org/conda-forge/noarch/tensorboard-2.13.0-pyhd8ed1ab_0.conda#321151b2405f11ec6681a9a6f30822b4 +https://conda.anaconda.org/conda-forge/noarch/conda-lock-1.0.5-pyhd8ed1ab_1.tar.bz2#1c31d380288fc1599fb5f4c76c8c828c https://conda.anaconda.org/conda-forge/noarch/jupyter-book-0.15.1-pyhd8ed1ab_0.conda#f10d556d3b3dc0aeae6aee37c412ea60 https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.0.0-pyhb4ecaf3_1.conda#a0be31e9bd84d6eae87cdbf74c56b90b https://conda.anaconda.org/conda-forge/noarch/notebook-6.5.4-pyha770c72_0.conda#ec4ce3ce0a55ce21b6f5b86049b97af9 @@ -461,4 +513,4 @@ https://conda.anaconda.org/conda-forge/noarch/torchinfo-1.8.0-pyhd8ed1ab_0.conda https://conda.anaconda.org/conda-forge/noarch/torchmetrics-0.11.4-pyhd8ed1ab_0.conda#480cb2b6d502003e937d9e4326bc398f https://conda.anaconda.org/pytorch/linux-64/torchtriton-2.0.0-py310.tar.bz2#e34aa90f6d7c20babf28fc9225b2a3eb https://conda.anaconda.org/pytorch/linux-64/torchvision-0.15.2-py310_cu118.tar.bz2#b38f7082cde2a86ca981194e9ef51028 -https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.0.4-pyhd8ed1ab_0.conda#ce9d626b181c6f8cceb5047f6a819f7d +https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.0.6-pyhd8ed1ab_0.conda#5325b6adf171d4d69968100af806994e diff --git a/conda/environment.linux-64.yml b/conda/environment.linux-64.yml index c5a18af..fa146c2 100644 --- a/conda/environment.linux-64.yml +++ b/conda/environment.linux-64.yml @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: c6bd68ba63788a00937c8cd1d91bb1e5813d242d7089005156ab1a663f53aee1 +# input_hash: 586016f05a089668afa3f0a057304e5826b41e87317e8d51969529896659d6a0 channels: - conda-forge @@ -9,7 +9,7 @@ channels: - nodefaults dependencies: - _libgcc_mutex=0.1=conda_forge - - ca-certificates=2023.5.7=hbcca054_0 + - ca-certificates=2023.7.22=hbcca054_0 - cuda-cudart=11.8.89=0 - cuda-cupti=11.8.87=0 - cuda-nvrtc=11.8.89=0 @@ -45,7 +45,7 @@ dependencies: - bzip2=1.0.8=h7f98852_4 - c-ares=1.19.1=hd590300_0 - double-conversion=3.2.0=h27087fc_1 - - eigen=3.4.1=h00ab1b0_0 + - eigen=3.4.0=h00ab1b0_0 - fftw=3.3.10=nompi_hc118613_108 - fribidi=1.0.10=h36c2ea0_0 - gettext=0.21.1=h27087fc_0 @@ -89,7 +89,7 @@ dependencies: - nettle=3.8.1=hc379101_1 - nspr=4.35=h27087fc_0 - openh264=2.3.1=hcb278e6_2 - - openssl=3.1.1=hd590300_1 + - openssl=3.1.2=hd590300_0 - pixman=0.40.0=h36c2ea0_0 - pthread-stubs=0.4=h36c2ea0_1001 - pugixml=1.11.4=h59595ed_1 @@ -170,23 +170,28 @@ dependencies: - xorg-libx11=1.8.4=h0b41bf4_0 - absl-py=1.4.0=pyhd8ed1ab_0 - alabaster=0.7.13=pyhd8ed1ab_0 + - appdirs=1.4.4=pyh9f0ad1d_0 - atk-1.0=2.38.0=hd4edc92_1 - attrs=21.4.0=pyhd8ed1ab_0 - backcall=0.2.0=pyh9f0ad1d_0 - backports=1.0=pyhd8ed1ab_3 - blinker=1.6.2=pyhd8ed1ab_0 + - boltons=23.0.0=pyhd8ed1ab_0 - brotli=1.0.9=h166bdaf_9 + - cached_property=1.5.2=pyha770c72_1 - cachetools=5.3.1=pyhd8ed1ab_0 - - certifi=2023.5.7=pyhd8ed1ab_0 + - certifi=2023.7.22=pyhd8ed1ab_0 - charset-normalizer=3.2.0=pyhd8ed1ab_0 - click=8.1.6=unix_pyh707e725_0 - colorama=0.4.6=pyhd8ed1ab_0 + - crashtest=0.4.1=pyhd8ed1ab_0 - cycler=0.11.0=pyhd8ed1ab_0 - dataclasses=0.8=pyhc8e2a94_3 - dbus=1.13.6=h5008d03_3 - - debugpy=1.6.7=py310heca2aa9_0 + - debugpy=1.6.8=py310hc6cd4ac_0 - decorator=5.1.1=pyhd8ed1ab_0 - defusedxml=0.7.1=pyhd8ed1ab_0 + - distlib=0.3.7=pyhd8ed1ab_0 - docutils=0.17.1=py310hff52083_3 - entrypoints=0.4=pyhd8ed1ab_0 - exceptiongroup=1.1.2=pyhd8ed1ab_0 @@ -206,23 +211,28 @@ dependencies: - imagesize=1.4.1=pyhd8ed1ab_0 - iniconfig=2.0.0=pyhd8ed1ab_0 - ipython_genutils=0.2.0=py_1 + - jeepney=0.8.0=pyhd8ed1ab_0 - jmespath=1.0.1=pyhd8ed1ab_0 + - jsonpointer=2.0=py_0 - jupyterlab_widgets=3.0.8=pyhd8ed1ab_0 - kiwisolver=1.4.4=py310hbf28c38_1 - lazy-object-proxy=1.9.0=py310h1fa729e_0 - lcms2=2.14=h6ed2654_0 - - libclang13=15.0.7=default_h9986a30_2 + - libclang13=15.0.7=default_h9986a30_3 - libcups=2.3.3=h36d4200_3 - libcurl=8.1.2=h409715c_0 - libpq=15.3=hbcd7760_1 - libsystemd0=253=h8c4010b_1 - libwebp=1.2.4=h522a892_0 + - lockfile=0.12.2=py_1 - loguru=0.7.0=py310hff52083_0 - markupsafe=2.1.3=py310h2372a71_0 - mccabe=0.7.0=pyhd8ed1ab_0 - mdurl=0.1.0=pyhd8ed1ab_0 - mistune=3.0.0=pyhd8ed1ab_0 + - more-itertools=10.1.0=pyhd8ed1ab_0 - mpmath=1.3.0=pyhd8ed1ab_0 + - msgpack-python=1.0.5=py310hdf3cbec_0 - multidict=6.0.4=py310h1fa729e_0 - munkres=1.1.4=pyh9f0ad1d_0 - mypy_extensions=1.0.0=pyha770c72_0 @@ -232,8 +242,9 @@ dependencies: - packaging=23.1=pyhd8ed1ab_0 - pandocfilters=1.5.0=pyhd8ed1ab_0 - parso=0.8.3=pyhd8ed1ab_0 - - pathspec=0.11.1=pyhd8ed1ab_0 + - pathspec=0.11.2=pyhd8ed1ab_0 - pickleshare=0.7.5=py_1003 + - pkginfo=1.9.6=pyhd8ed1ab_0 - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0 - pluggy=1.2.0=pyhd8ed1ab_0 - ply=3.11=py_1 @@ -243,6 +254,7 @@ dependencies: - pure_eval=0.2.2=pyhd8ed1ab_0 - pyasn1=0.4.8=py_0 - pycodestyle=2.10.0=pyhd8ed1ab_0 + - pycosat=0.6.4=py310h5764c6d_1 - pycparser=2.21=pyhd8ed1ab_0 - pyflakes=3.0.1=pyhd8ed1ab_0 - pygments=2.15.1=pyhd8ed1ab_0 @@ -250,7 +262,8 @@ dependencies: - pyparsing=3.0.9=pyhd8ed1ab_0 - pyrsistent=0.19.3=py310h1fa729e_0 - pysocks=1.7.1=pyha2e5f31_6 - - python-fastjsonschema=2.17.1=pyhd8ed1ab_0 + - python-fastjsonschema=2.18.0=pyhd8ed1ab_0 + - python-installer=0.7.0=pyhd8ed1ab_0 - python-json-logger=2.0.7=pyhd8ed1ab_0 - pytorch-cuda=11.8=h7e8668a_5 - pytz=2023.3=pyhd8ed1ab_0 @@ -260,6 +273,7 @@ dependencies: - ruamel.yaml.clib=0.2.7=py310h1fa729e_1 - send2trash=1.8.2=pyh41d4057_0 - setuptools=67.7.2=pyhd8ed1ab_0 + - shellingham=1.5.1=pyhd8ed1ab_0 - six=1.16.0=pyh6c4a22f_0 - sniffio=1.3.0=pyhd8ed1ab_0 - snowballstemmer=2.2.0=pyhd8ed1ab_0 @@ -275,17 +289,23 @@ dependencies: - tensorboard-data-server=0.7.0=py310h34c0648_0 - toml=0.10.2=pyhd8ed1ab_0 - tomli=2.0.1=pyhd8ed1ab_0 + - tomlkit=0.12.1=pyha770c72_0 + - toolz=0.12.0=pyhd8ed1ab_0 - tornado=6.3.2=py310h2372a71_0 - traitlets=5.9.0=pyhd8ed1ab_0 + - trove-classifiers=2023.7.6=pyhd8ed1ab_0 - typed-ast=1.5.5=py310h2372a71_0 + - typing=3.10.0.0=pyhd8ed1ab_0 - typing_extensions=4.7.1=pyha770c72_0 - typing_utils=0.1.0=pyhd8ed1ab_0 - uc-micro-py=1.0.1=pyhd8ed1ab_0 - unicodedata2=15.0.0=py310h5764c6d_0 - unidecode=1.3.6=pyhd8ed1ab_0 + - uri-template=1.3.0=pyhd8ed1ab_0 + - webcolors=1.13=pyhd8ed1ab_0 - webencodings=0.5.1=py_1 - websocket-client=1.6.1=pyhd8ed1ab_0 - - wheel=0.40.0=pyhd8ed1ab_1 + - wheel=0.41.0=pyhd8ed1ab_0 - widgetsnbextension=4.0.8=pyhd8ed1ab_0 - wrapt=1.15.0=py310h1fa729e_0 - xcb-util-image=0.4.0=h166bdaf_0 @@ -299,27 +319,33 @@ dependencies: - anyio=3.7.1=pyhd8ed1ab_0 - asttokens=2.2.1=pyhd8ed1ab_0 - babel=2.12.1=pyhd8ed1ab_1 + - backports.cached-property=1.0.2=pyhd8ed1ab_0 - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 - beautifulsoup4=4.12.2=pyha770c72_0 - bleach=6.0.0=pyhd8ed1ab_0 + - cached-property=1.5.2=hd8ed1ab_1 - cairo=1.16.0=ha61ee94_1014 - cffi=1.15.1=py310h255011f_3 - - comm=0.1.3=pyhd8ed1ab_0 + - click-default-group=1.2.2=pyhd8ed1ab_1 + - comm=0.1.4=pyhd8ed1ab_0 - curl=8.1.2=h409715c_0 - dacite=1.8.0=pyhd8ed1ab_0 - deprecation=2.1.0=pyh9f0ad1d_0 - flake8=6.0.0=pyhd8ed1ab_0 - - fonttools=4.41.0=py310h2372a71_0 + - fonttools=4.42.0=py310h2372a71_0 - glew=2.1.0=h9c3ff4c_2 - glib=2.76.4=hfc55251_0 - hdf5=1.12.2=nompi_h4df4325_101 + - html5lib=1.1=pyh9f0ad1d_0 - importlib-metadata=6.8.0=pyha770c72_0 - importlib_resources=6.0.0=pyhd8ed1ab_1 - - jedi=0.18.2=pyhd8ed1ab_0 + - jaraco.classes=3.3.0=pyhd8ed1ab_0 + - jedi=0.19.0=pyhd8ed1ab_0 - jinja2=3.1.2=pyhd8ed1ab_1 + - jsonpatch=1.32=pyhd8ed1ab_0 - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 - latexcodec=2.0.1=pyh9f0ad1d_0 - - libclang=15.0.7=default_h7634d5b_2 + - libclang=15.0.7=default_h7634d5b_3 - libgd=2.3.3=h18fbbfe_3 - libva=2.18.0=h0b41bf4_0 - lightning-utilities=0.9.0=pyhd8ed1ab_0 @@ -343,7 +369,7 @@ dependencies: - rfc3339-validator=0.1.4=pyhd8ed1ab_0 - rsa=4.9=pyhd8ed1ab_0 - ruamel.yaml=0.17.32=py310h2372a71_0 - - sip=6.7.9=py310hc6cd4ac_0 + - sip=6.7.11=py310hc6cd4ac_0 - sympy=1.12=pypyh9d50eac_103 - tbb-devel=2021.9.0=hf52228f_0 - terminado=0.17.1=pyh41d4057_0 @@ -352,12 +378,15 @@ dependencies: - typing-extensions=4.7.1=hd8ed1ab_0 - werkzeug=2.3.6=pyhd8ed1ab_0 - yarl=1.9.2=py310h2372a71_0 + - annotated-types=0.5.0=pyhd8ed1ab_0 - argon2-cffi-bindings=21.2.0=py310h5764c6d_3 + - arrow=1.2.3=pyhd8ed1ab_0 - astroid=2.15.6=py310hff52083_0 - async-timeout=4.0.2=pyhd8ed1ab_0 - brotlipy=0.7.0=py310h5764c6d_1005 - cryptography=41.0.2=py310h75e40e8_0 - ffmpeg=5.1.2=gpl_h8dda1f0_106 + - fqdn=1.5.1=pyhd8ed1ab_0 - ghp-import=2.1.0=pyhd8ed1ab_0 - gstreamer=1.22.0=h25f0c4b_2 - harfbuzz=6.0.0=h8e241bc_0 @@ -367,40 +396,51 @@ dependencies: - libblas=3.9.0=16_linux64_mkl - libitk=5.3.0=hcedbc38_0 - libnetcdf=4.8.1=nompi_h261ec11_106 - - markdown=3.4.3=pyhd8ed1ab_0 + - markdown=3.4.4=pyhd8ed1ab_0 - mdit-py-plugins=0.4.0=pyhd8ed1ab_0 - mkl-devel=2022.1.0=ha770c72_916 - - platformdirs=3.9.1=pyhd8ed1ab_0 + - platformdirs=3.10.0=pyhd8ed1ab_0 + - poetry-core=1.6.1=pyhd8ed1ab_0 - pulseaudio-daemon=16.1=ha8d29e2_3 - pybtex=0.24.0=pyhd8ed1ab_2 - - pyqt5-sip=12.11.0=py310heca2aa9_3 + - pydantic-core=2.4.0=py310hcb5633a_0 + - pyqt5-sip=12.12.2=py310hc6cd4ac_4 - python-build=0.10.0=pyhd8ed1ab_1 - setuptools-scm=7.1.0=pyhd8ed1ab_0 - sqlalchemy=2.0.19=py310h2372a71_0 - stack_data=0.6.2=pyhd8ed1ab_0 - wcwidth=0.2.6=pyhd8ed1ab_0 + - zstandard=0.19.0=py310h1275a96_2 - aiohttp=3.8.5=py310h2372a71_0 - argon2-cffi=21.3.0=pyhd8ed1ab_0 - black=22.3.0=pyhd8ed1ab_0 + - conda-package-streaming=0.9.0=pyhd8ed1ab_0 - gst-plugins-base=1.22.0=h4243ec0_2 + - isoduration=20.11.0=pyhd8ed1ab_0 - jupyter_core=5.3.1=py310hff52083_0 - - jupyter_events=0.6.3=pyhd8ed1ab_0 - libcblas=3.9.0=16_linux64_mkl - liblapack=3.9.0=16_linux64_mkl - oauthlib=3.2.2=pyhd8ed1ab_0 - pango=1.50.14=hd33c08f_0 + - poetry-plugin-export=1.4.0=pyhd8ed1ab_0 - prompt-toolkit=3.0.39=pyha770c72_0 - pulseaudio=16.1=hcb278e6_3 - pybtex-docutils=1.0.2=py310hff52083_2 + - pydantic=2.1.1=pyhd8ed1ab_0 - pyopenssl=23.2.0=pyhd8ed1ab_1 + - secretstorage=3.3.3=py310hff52083_1 - simpleitk=2.2.1=py310h2b9ea3a_1 + - virtualenv=20.24.2=pyhd8ed1ab_0 + - conda-package-handling=2.2.0=pyh38be061_0 - flake8-black=0.3.6=pyhd8ed1ab_0 - gtk2=2.24.33=h90689f9_2 + - jsonschema-with-format-nongpl=4.17.3=pyhd8ed1ab_0 - jupyter_client=8.3.0=pyhd8ed1ab_0 + - keyring=23.13.1=py310hff52083_0 - liblapacke=3.9.0=16_linux64_mkl - librsvg=2.54.4=h7abd40a_0 - - nbformat=5.9.1=pyhd8ed1ab_0 - - numpy=1.25.1=py310ha4c1d20_0 + - nbformat=5.9.2=pyhd8ed1ab_0 + - numpy=1.25.2=py310ha4c1d20_0 - prompt_toolkit=3.0.39=hd8ed1ab_0 - qt-main=5.15.8=h5d23da1_6 - urllib3=1.26.15=pyhd8ed1ab_0 @@ -408,32 +448,42 @@ dependencies: - blas-devel=3.9.0=16_linux64_mkl - botocore=1.29.165=pyhd8ed1ab_0 - contourpy=1.1.0=py310hd41b1e2_0 + - dulwich=0.21.5=py310h2372a71_0 - graphviz=7.0.5=h2e5815a_0 - ipython=8.14.0=pyh41d4057_0 + - jupyter_events=0.7.0=pyhd8ed1ab_0 - nbclient=0.7.4=pyhd8ed1ab_0 - nibabel=5.1.0=py310hff52083_2 - pandas=1.5.3=py310h9b08913_1 - - pyqt=5.15.7=py310hab646b1_3 + - pyqt=5.15.9=py310h04931ad_4 + - rapidfuzz=2.15.1=py310heca2aa9_0 - requests=2.31.0=pyhd8ed1ab_0 - vtk=9.2.5=qt_py310hc895abb_200 - blas=2.116=mkl + - cachecontrol=0.12.14=pyhd8ed1ab_0 + - cleo=2.0.1=pyhd8ed1ab_0 + - conda=23.7.2=py310hff52083_0 + - ensureconda=1.4.3=pyhd8ed1ab_0 - google-auth=2.22.0=pyh1a96a4e_0 - ipykernel=6.23.3=pyh71e2992_0 + - ipywidgets=8.1.0=pyhd8ed1ab_0 - jupyter-cache=0.6.1=pyhd8ed1ab_0 - matplotlib-base=3.7.2=py310hf38f957_0 - - nbconvert-core=7.7.1=pyhd8ed1ab_1 + - nbconvert-core=7.7.3=pyhd8ed1ab_0 - pooch=1.7.0=pyha770c72_3 - requests-oauthlib=1.3.1=pyhd8ed1ab_0 + - requests-toolbelt=1.0.0=pyhd8ed1ab_0 - s3transfer=0.6.1=pyhd8ed1ab_0 - sphinx=4.5.0=pyh6c4a22f_0 - boto3=1.26.165=pyhd8ed1ab_0 + - cachecontrol-with-filecache=0.12.14=pyhd8ed1ab_0 + - conda-devenv=2.3.0=pyhd8ed1ab_0 - google-auth-oauthlib=1.0.0=pyhd8ed1ab_1 - - ipywidgets=8.0.7=pyhd8ed1ab_0 - jupyter_console=6.6.3=pyhd8ed1ab_0 - jupyter_server=2.7.0=pyhd8ed1ab_0 - matplotlib=3.7.2=py310hff52083_0 - myst-parser=0.18.1=pyhd8ed1ab_0 - - nbconvert-pandoc=7.7.1=pyhd8ed1ab_1 + - nbconvert-pandoc=7.7.3=pyhd8ed1ab_0 - pydata-sphinx-theme=0.13.3=pyhd8ed1ab_0 - qtconsole-base=5.4.3=pyha770c72_0 - scipy=1.10.1=py310ha4c1d20_3 @@ -451,13 +501,15 @@ dependencies: - sphinxcontrib-golangdomain=0.2.0.dev0=py_0 - sphinxcontrib-jquery=4.1=pyhd8ed1ab_0 - myst-nb=0.17.2=pyhd8ed1ab_0 - - nbconvert=7.7.1=pyhd8ed1ab_1 + - nbconvert=7.7.3=pyhd8ed1ab_0 - notebook-shim=0.2.3=pyhd8ed1ab_0 + - poetry=1.5.1=linux_pyhd8ed1ab_0 - qtconsole=5.4.3=pyhd8ed1ab_0 - sphinx-autoapi=2.1.0=pyhd8ed1ab_0 - sphinx-book-theme=1.0.1=pyhd8ed1ab_0 - sphinx_rtd_theme=1.2.2=pyha770c72_0 - tensorboard=2.13.0=pyhd8ed1ab_0 + - conda-lock=1.0.5=pyhd8ed1ab_1 - jupyter-book=0.15.1=pyhd8ed1ab_0 - nbclassic=1.0.0=pyhb4ecaf3_1 - notebook=6.5.4=pyha770c72_0 @@ -467,4 +519,4 @@ dependencies: - torchmetrics=0.11.4=pyhd8ed1ab_0 - torchtriton=2.0.0=py310 - torchvision=0.15.2=py310_cu118 - - pytorch-lightning=2.0.4=pyhd8ed1ab_0 + - pytorch-lightning=2.0.6=pyhd8ed1ab_0 diff --git a/conda/environment.osx-64.lock b/conda/environment.osx-64.lock index 47ab52e..50182b2 100644 --- a/conda/environment.osx-64.lock +++ b/conda/environment.osx-64.lock @@ -1,10 +1,10 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: 533a7567b393584157366e71374225596e814fe74cfcb03642d3b4e184d58c87 +# input_hash: 1e6e6cea02ff8fd576a8852899876561e48ebb709abcd877d8d931d3b50338da @EXPLICIT https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-h0d85af4_4.tar.bz2#37edc4e6304ca87316e160f5ca0bd1b5 https://conda.anaconda.org/conda-forge/osx-64/c-ares-1.19.1-h0dc2134_0.conda#b3e62631b4e1b9801477523ce1d6f355 -https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2023.5.7-h8857fd0_0.conda#b704e4b79ba0d887c4870b7b09d6a4df +https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2023.7.22-h8857fd0_0.conda#bf2c54c18997bf3542af074c10191771 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb @@ -45,7 +45,7 @@ https://conda.anaconda.org/conda-forge/osx-64/xz-5.2.6-h775f41a_0.tar.bz2#a72f9d https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h0d85af4_2.tar.bz2#d7e08fcf8259d742156188e8762b4d20 https://conda.anaconda.org/conda-forge/osx-64/aom-3.5.0-hf0c8a7f_0.tar.bz2#9110390ac33346f643e26051a92de5ce https://conda.anaconda.org/conda-forge/osx-64/double-conversion-3.2.0-hf0c8a7f_1.tar.bz2#3c2d7d657d83eac1507bc6fbab9eb297 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-1,6 +1,6 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: 533a7567b393584157366e71374225596e814fe74cfcb03642d3b4e184d58c87 +# input_hash: 1e6e6cea02ff8fd576a8852899876561e48ebb709abcd877d8d931d3b50338da channels: - conda-forge @@ -10,7 +10,7 @@ channels: dependencies: - bzip2=1.0.8=h0d85af4_4 - c-ares=1.19.1=h0dc2134_0 - - ca-certificates=2023.5.7=h8857fd0_0 + - ca-certificates=2023.7.22=h8857fd0_0 - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - font-ttf-inconsolata=3.000=h77eed37_0 - font-ttf-source-code-pro=2.038=h77eed37_0 @@ -51,7 +51,7 @@ dependencies: - yaml=0.2.5=h0d85af4_2 - aom=3.5.0=hf0c8a7f_0 - double-conversion=3.2.0=hf0c8a7f_1 - - eigen=3.4.1=h1c7c39f_0 + - eigen=3.4.0=h1c7c39f_0 - expat=2.5.0=hf0c8a7f_1 - fonts-conda-forge=1=0 - gettext=0.21.1=h8a4c099_0 @@ -66,7 +66,7 @@ dependencies: - libbrotlidec=1.0.9=hb7f2c08_9 - libbrotlienc=1.0.9=hb7f2c08_9 - libedit=3.1.20191231=h0678c8f_2 - - libgfortran5=12.2.0=he409387_31 + - libgfortran5=12.3.0=hbd3c1fe_1 - libllvm13=13.0.1=h64f94b2_2 - libpng=1.6.39=ha978bb4_0 - libsqlite=3.42.0=h58db7d2_0 @@ -76,7 +76,7 @@ dependencies: - lz4-c=1.9.4=hf0c8a7f_0 - nspr=4.35=hea0b92c_0 - openh264=2.3.1=hf0c8a7f_2 - - openssl=3.1.1=h8a1eda9_1 + - openssl=3.1.2=h8a1eda9_0 - p11-kit=0.24.1=h65f8906_0 - pandoc=3.1.3=h9d075a6_0 - pcre2=10.40=h1c4e4bc_0 @@ -84,7 +84,7 @@ dependencies: - re2=2023.03.02=h096449b_0 - readline=8.2=h9e318b2_1 - svt-av1=1.4.1=hf0c8a7f_0 - - tbb=2021.9.0=hb8565cd_0 + - tbb=2021.10.0=h1c7c39f_0 - tk=8.6.12=h5dbffcc_0 - x265=3.5=hbb4e6a2_3 - zeromq=4.3.4=he49afe7_1 @@ -96,8 +96,8 @@ dependencies: - gl2ps=1.4.2=h4cff582_0 - hdf4=4.2.15=h7aa5921_5 - krb5=1.20.1=h049b76e_0 - - libclang=13.0.1=default_h255f2f3_1 - - libgfortran=5.0.0=11_3_0_h97931a8_31 + - libclang=13.0.1=root_62804_h2961583_3 + - libgfortran=5.0.0=12_3_0_h97931a8_1 - libglib=2.76.4=hc62aa5d_0 - libidn2=2.3.4=hb7f2c08_0 - libnghttp2=1.52.0=he2ab024_0 @@ -113,26 +113,31 @@ dependencies: - nss=3.89=h78b00b3_0 - python=3.10.12=had23ca6_0_cpython - sqlite=3.42.0=h2b0dec6_0 - - tbb-devel=2021.9.0=hb8565cd_0 + - tbb-devel=2021.10.0=h1c7c39f_0 - absl-py=1.4.0=pyhd8ed1ab_0 - alabaster=0.7.13=pyhd8ed1ab_0 + - appdirs=1.4.4=pyh9f0ad1d_0 - appnope=0.1.3=pyhd8ed1ab_0 - atk-1.0=2.38.0=h1d18e73_1 - attrs=21.4.0=pyhd8ed1ab_0 - backcall=0.2.0=pyh9f0ad1d_0 - backports=1.0=pyhd8ed1ab_3 - blinker=1.6.2=pyhd8ed1ab_0 + - boltons=23.0.0=pyhd8ed1ab_0 - brotli=1.0.9=hb7f2c08_9 + - cached_property=1.5.2=pyha770c72_1 - cachetools=5.3.1=pyhd8ed1ab_0 - - certifi=2023.5.7=pyhd8ed1ab_0 + - certifi=2023.7.22=pyhd8ed1ab_0 - charset-normalizer=3.2.0=pyhd8ed1ab_0 - click=8.1.6=unix_pyh707e725_0 - colorama=0.4.6=pyhd8ed1ab_0 + - crashtest=0.4.1=pyhd8ed1ab_0 - cycler=0.11.0=pyhd8ed1ab_0 - dataclasses=0.8=pyhc8e2a94_3 - - debugpy=1.6.7=py310h7a76584_0 + - debugpy=1.6.8=py310h9e9d8ca_0 - decorator=5.1.1=pyhd8ed1ab_0 - defusedxml=0.7.1=pyhd8ed1ab_0 + - distlib=0.3.7=pyhd8ed1ab_0 - docutils=0.17.1=py310h2ec42d9_3 - entrypoints=0.4=pyhd8ed1ab_0 - exceptiongroup=1.1.2=pyhd8ed1ab_0 @@ -153,6 +158,7 @@ dependencies: - iniconfig=2.0.0=pyhd8ed1ab_0 - ipython_genutils=0.2.0=py_1 - jmespath=1.0.1=pyhd8ed1ab_0 + - jsonpointer=2.0=py_0 - jupyterlab_widgets=3.0.8=pyhd8ed1ab_0 - kiwisolver=1.4.4=py310ha23aa8a_1 - lazy-object-proxy=1.9.0=py310h90acd4f_0 @@ -162,14 +168,17 @@ dependencies: - libgrpc=1.56.2=he6801ca_0 - libpq=15.3=h9dc22bb_1 - libwebp=1.2.4=hfa4350a_0 + - lockfile=0.12.2=py_1 - loguru=0.7.0=py310h2ec42d9_0 - markupsafe=2.1.3=py310h6729b98_0 - mccabe=0.7.0=pyhd8ed1ab_0 - mdurl=0.1.0=pyhd8ed1ab_0 - mistune=3.0.0=pyhd8ed1ab_0 - mkl-devel=2022.1.0=h694c41f_929 + - more-itertools=10.1.0=pyhd8ed1ab_0 - mpc=1.3.1=h81bd1dd_0 - mpmath=1.3.0=pyhd8ed1ab_0 + - msgpack-python=1.0.5=py310ha23aa8a_0 - multidict=6.0.4=py310h90acd4f_0 - munkres=1.1.4=pyh9f0ad1d_0 - mypy_extensions=1.0.0=pyha770c72_0 @@ -180,8 +189,9 @@ dependencies: - packaging=23.1=pyhd8ed1ab_0 - pandocfilters=1.5.0=pyhd8ed1ab_0 - parso=0.8.3=pyhd8ed1ab_0 - - pathspec=0.11.1=pyhd8ed1ab_0 + - pathspec=0.11.2=pyhd8ed1ab_0 - pickleshare=0.7.5=py_1003 + - pkginfo=1.9.6=pyhd8ed1ab_0 - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0 - pluggy=1.2.0=pyhd8ed1ab_0 - ply=3.11=py_1 @@ -191,6 +201,7 @@ dependencies: - pure_eval=0.2.2=pyhd8ed1ab_0 - pyasn1=0.4.8=py_0 - pycodestyle=2.10.0=pyhd8ed1ab_0 + - pycosat=0.6.4=py310h90acd4f_1 - pycparser=2.21=pyhd8ed1ab_0 - pyflakes=3.0.1=pyhd8ed1ab_0 - pygments=2.15.1=pyhd8ed1ab_0 @@ -198,7 +209,8 @@ dependencies: - pyparsing=3.0.9=pyhd8ed1ab_0 - pyrsistent=0.19.3=py310h90acd4f_0 - pysocks=1.7.1=pyha2e5f31_6 - - python-fastjsonschema=2.17.1=pyhd8ed1ab_0 + - python-fastjsonschema=2.18.0=pyhd8ed1ab_0 + - python-installer=0.7.0=pyhd8ed1ab_0 - python-json-logger=2.0.7=pyhd8ed1ab_0 - pytz=2023.3=pyhd8ed1ab_0 - pyyaml=6.0=py310h90acd4f_5 @@ -206,6 +218,7 @@ dependencies: - rfc3986-validator=0.1.1=pyh9f0ad1d_0 - ruamel.yaml.clib=0.2.7=py310h90acd4f_1 - setuptools=67.7.2=pyhd8ed1ab_0 + - shellingham=1.5.1=pyhd8ed1ab_0 - six=1.16.0=pyh6c4a22f_0 - sniffio=1.3.0=pyhd8ed1ab_0 - snowballstemmer=2.2.0=pyhd8ed1ab_0 @@ -220,17 +233,23 @@ dependencies: - tensorboard-data-server=0.7.0=py310hdd0c95c_0 - toml=0.10.2=pyhd8ed1ab_0 - tomli=2.0.1=pyhd8ed1ab_0 + - tomlkit=0.12.1=pyha770c72_0 + - toolz=0.12.0=pyhd8ed1ab_0 - tornado=6.3.2=py310h6729b98_0 - traitlets=5.9.0=pyhd8ed1ab_0 + - trove-classifiers=2023.7.6=pyhd8ed1ab_0 - typed-ast=1.5.4=py310h90acd4f_1 + - typing=3.10.0.0=pyhd8ed1ab_0 - typing_extensions=4.7.1=pyha770c72_0 - typing_utils=0.1.0=pyhd8ed1ab_0 - uc-micro-py=1.0.1=pyhd8ed1ab_0 - unicodedata2=15.0.0=py310h90acd4f_0 - unidecode=1.3.6=pyhd8ed1ab_0 + - uri-template=1.3.0=pyhd8ed1ab_0 + - webcolors=1.13=pyhd8ed1ab_0 - webencodings=0.5.1=py_1 - websocket-client=1.6.1=pyhd8ed1ab_0 - - wheel=0.40.0=pyhd8ed1ab_1 + - wheel=0.41.0=pyhd8ed1ab_0 - widgetsnbextension=4.0.8=pyhd8ed1ab_0 - wrapt=1.15.0=py310h90acd4f_0 - zipp=3.16.2=pyhd8ed1ab_0 @@ -239,26 +258,32 @@ dependencies: - anyio=3.7.1=pyhd8ed1ab_0 - asttokens=2.2.1=pyhd8ed1ab_0 - babel=2.12.1=pyhd8ed1ab_1 + - backports.cached-property=1.0.2=pyhd8ed1ab_0 - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 - beautifulsoup4=4.12.2=pyha770c72_0 - bleach=6.0.0=pyhd8ed1ab_0 + - cached-property=1.5.2=hd8ed1ab_1 - cairo=1.16.0=h904041c_1014 - cffi=1.15.1=py310ha78151a_3 - - comm=0.1.3=pyhd8ed1ab_0 + - click-default-group=1.2.2=pyhd8ed1ab_1 + - comm=0.1.4=pyhd8ed1ab_0 - curl=8.1.2=hbee3ae8_0 - dacite=1.8.0=pyhd8ed1ab_0 - deprecation=2.1.0=pyh9f0ad1d_0 - ffmpeg=5.1.2=gpl_h8b4fe81_106 - flake8=6.0.0=pyhd8ed1ab_0 - - fonttools=4.41.0=py310h6729b98_0 + - fonttools=4.42.0=py310h6729b98_0 - glib=2.76.4=h7d26f99_0 - gmpy2=2.1.2=py310hb691cb2_1 - grpcio=1.56.2=py310h0d4bf3c_0 - hdf5=1.12.2=nompi_h48135f9_101 + - html5lib=1.1=pyh9f0ad1d_0 - importlib-metadata=6.8.0=pyha770c72_0 - importlib_resources=6.0.0=pyhd8ed1ab_1 - - jedi=0.18.2=pyhd8ed1ab_0 + - jaraco.classes=3.3.0=pyhd8ed1ab_0 + - jedi=0.19.0=pyhd8ed1ab_0 - jinja2=3.1.2=pyhd8ed1ab_1 + - jsonpatch=1.32=pyhd8ed1ab_0 - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 - latexcodec=2.0.1=pyh9f0ad1d_0 - libcblas=3.9.0=17_osx64_mkl @@ -284,20 +309,23 @@ dependencies: - rfc3339-validator=0.1.4=pyhd8ed1ab_0 - rsa=4.9=pyhd8ed1ab_0 - ruamel.yaml=0.17.32=py310h6729b98_0 - - sip=6.7.9=py310h9e9d8ca_0 + - sip=6.7.11=py310h9e9d8ca_0 - terminado=0.17.1=pyhd1c38e8_0 - tinycss2=1.2.1=pyhd8ed1ab_0 - tqdm=4.65.0=pyhd8ed1ab_1 - typing-extensions=4.7.1=hd8ed1ab_0 - werkzeug=2.3.6=pyhd8ed1ab_0 - yarl=1.9.2=py310h6729b98_0 + - annotated-types=0.5.0=pyhd8ed1ab_0 - argon2-cffi-bindings=21.2.0=py310h90acd4f_3 + - arrow=1.2.3=pyhd8ed1ab_0 - astroid=2.15.6=py310h2ec42d9_0 - async-timeout=4.0.2=pyhd8ed1ab_0 - brotlipy=0.7.0=py310h90acd4f_1005 - cryptography=41.0.2=py310ha1817de_0 + - fqdn=1.5.1=pyhd8ed1ab_0 - ghp-import=2.1.0=pyhd8ed1ab_0 - - gstreamer=1.22.4=h840fbdc_1 + - gstreamer=1.22.5=h840fbdc_0 - harfbuzz=6.0.0=h08f8713_0 - importlib_metadata=6.8.0=hd8ed1ab_0 - jsonschema=4.17.3=pyhd8ed1ab_0 @@ -305,76 +333,97 @@ dependencies: - libitk=5.3.0=h10ab89a_0 - liblapacke=3.9.0=17_osx64_mkl - libnetcdf=4.8.1=nompi_hc61b76e_106 - - markdown=3.4.3=pyhd8ed1ab_0 + - markdown=3.4.4=pyhd8ed1ab_0 - mdit-py-plugins=0.4.0=pyhd8ed1ab_0 - - numpy=1.25.1=py310h7451ae0_0 - - platformdirs=3.9.1=pyhd8ed1ab_0 + - numpy=1.25.2=py310h7451ae0_0 + - platformdirs=3.10.0=pyhd8ed1ab_0 + - poetry-core=1.6.1=pyhd8ed1ab_0 - pybtex=0.24.0=pyhd8ed1ab_2 + - pydantic-core=2.4.0=py310h3461e44_0 - pyobjc-framework-cocoa=9.2=py310hef2d279_0 - - pyqt5-sip=12.11.0=py310h415000c_3 + - pyqt5-sip=12.12.2=py310h018f80b_4 - python-build=0.10.0=pyhd8ed1ab_1 - setuptools-scm=7.1.0=pyhd8ed1ab_0 - sqlalchemy=2.0.19=py310h6729b98_0 - stack_data=0.6.2=pyhd8ed1ab_0 - sympy=1.12=pypyh9d50eac_103 - wcwidth=0.2.6=pyhd8ed1ab_0 + - xattr=0.10.1=py310h90acd4f_0 + - zstandard=0.19.0=py310h151724a_2 - aiohttp=3.8.5=py310h6729b98_0 - argon2-cffi=21.3.0=pyhd8ed1ab_0 - black=22.3.0=pyhd8ed1ab_0 - blas-devel=3.9.0=17_osx64_mkl + - conda-package-streaming=0.9.0=pyhd8ed1ab_0 - contourpy=1.1.0=py310h88cfcbd_0 - - gst-plugins-base=1.22.4=hb5d3a86_1 + - gst-plugins-base=1.22.5=hb5d3a86_0 + - isoduration=20.11.0=pyhd8ed1ab_0 - jupyter_core=5.3.1=py310h2ec42d9_0 - - jupyter_events=0.6.3=pyhd8ed1ab_0 + - keyring=23.13.1=py310h2ec42d9_0 - nibabel=5.1.0=py310h2ec42d9_2 - oauthlib=3.2.2=pyhd8ed1ab_0 - pandas=1.5.3=py310hecf8f37_1 - pango=1.50.14=hbd9bf65_0 + - poetry-plugin-export=1.4.0=pyhd8ed1ab_0 - prompt-toolkit=3.0.39=pyha770c72_0 - pybtex-docutils=1.0.2=py310h2ec42d9_2 + - pydantic=2.1.1=pyhd8ed1ab_0 - pyopenssl=23.2.0=pyhd8ed1ab_1 + - rapidfuzz=2.15.1=py310h7a76584_0 - send2trash=1.8.2=pyhd1c38e8_0 - simpleitk=2.2.1=py310h4447650_1 + - virtualenv=20.24.2=pyhd8ed1ab_0 - blas=2.117=mkl + - cleo=2.0.1=pyhd8ed1ab_0 + - conda-package-handling=2.2.0=pyh38be061_0 - flake8-black=0.3.6=pyhd8ed1ab_0 - gtk2=2.24.33=h7c1209e_2 + - jsonschema-with-format-nongpl=4.17.3=pyhd8ed1ab_0 - jupyter_client=8.3.0=pyhd8ed1ab_0 - librsvg=2.54.4=h3d48ba6_0 - matplotlib-base=3.7.2=py310h475a17b_0 - - nbformat=5.9.1=pyhd8ed1ab_0 + - nbformat=5.9.2=pyhd8ed1ab_0 - prompt_toolkit=3.0.39=hd8ed1ab_0 - qt-main=5.15.8=h1d3b3f8_6 - urllib3=1.26.15=pyhd8ed1ab_0 - wslink=1.11.1=pyhd8ed1ab_0 - botocore=1.29.165=pyhd8ed1ab_0 + - dulwich=0.21.5=py310h6729b98_0 - graphviz=7.0.5=hc51f7b9_0 - ipython=8.14.0=pyhd1c38e8_0 + - jupyter_events=0.7.0=pyhd8ed1ab_0 - matplotlib=3.7.2=py310h2ec42d9_0 - nbclient=0.7.4=pyhd8ed1ab_0 - - pyqt=5.15.7=py310hdd03f62_3 + - pyqt=5.15.9=py310hecc045f_4 - pytorch=2.0.1=py3.10_0 - requests=2.31.0=pyhd8ed1ab_0 - vtk=9.2.5=qt_py310hea5b068_200 + - cachecontrol=0.12.14=pyhd8ed1ab_0 + - conda=23.7.2=py310h2ec42d9_0 + - ensureconda=1.4.3=pyhd8ed1ab_0 - google-auth=2.22.0=pyh1a96a4e_0 - ipykernel=6.23.3=pyh5fb750a_0 + - ipywidgets=8.1.0=pyhd8ed1ab_0 - jupyter-cache=0.6.1=pyhd8ed1ab_0 - - nbconvert-core=7.7.1=pyhd8ed1ab_1 + - nbconvert-core=7.7.3=pyhd8ed1ab_0 - pooch=1.7.0=pyha770c72_3 - requests-oauthlib=1.3.1=pyhd8ed1ab_0 + - requests-toolbelt=1.0.0=pyhd8ed1ab_0 - s3transfer=0.6.1=pyhd8ed1ab_0 - sphinx=4.5.0=pyh6c4a22f_0 - torchinfo=1.8.0=pyhd8ed1ab_0 - torchmetrics=0.11.4=pyhd8ed1ab_0 - torchvision=0.15.2=py310_cpu - boto3=1.26.165=pyhd8ed1ab_0 + - cachecontrol-with-filecache=0.12.14=pyhd8ed1ab_0 + - conda-devenv=2.3.0=pyhd8ed1ab_0 - google-auth-oauthlib=1.0.0=pyhd8ed1ab_1 - - ipywidgets=8.0.7=pyhd8ed1ab_0 - jupyter_console=6.6.3=pyhd8ed1ab_0 - jupyter_server=2.7.0=pyhd8ed1ab_0 - myst-parser=0.18.1=pyhd8ed1ab_0 - - nbconvert-pandoc=7.7.1=pyhd8ed1ab_1 + - nbconvert-pandoc=7.7.3=pyhd8ed1ab_0 - pydata-sphinx-theme=0.13.3=pyhd8ed1ab_0 - - pytorch-lightning=2.0.4=pyhd8ed1ab_0 + - pytorch-lightning=2.0.6=pyhd8ed1ab_0 - qtconsole-base=5.4.3=pyha770c72_0 - scipy=1.10.1=py310h3900cf1_3 - sphinx-comments=0.0.3=pyh9f0ad1d_0 @@ -391,13 +440,15 @@ dependencies: - sphinxcontrib-golangdomain=0.2.0.dev0=py_0 - sphinxcontrib-jquery=4.1=pyhd8ed1ab_0 - 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https://conda.anaconda.org/conda-forge/noarch/notebook-6.5.4-pyha770c72_0.conda#ec4ce3ce0a55ce21b6f5b86049b97af9 -https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.0.4-pyhd8ed1ab_0.conda#ce9d626b181c6f8cceb5047f6a819f7d +https://conda.anaconda.org/conda-forge/noarch/pytorch-lightning-2.0.6-pyhd8ed1ab_0.conda#5325b6adf171d4d69968100af806994e https://conda.anaconda.org/conda-forge/win-64/jupyter-1.0.0-py310h5588dad_8.conda#5fe66001841554f8b30f7db775d9ba81 diff --git a/conda/environment.win-64.yml b/conda/environment.win-64.yml index b0a956a..f2172f5 100644 --- a/conda/environment.win-64.yml +++ b/conda/environment.win-64.yml @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: win-64 -# input_hash: 6255d416b6866feefaa84cbaf27b3a7608f8bb60e8d5e51ca00574e0f3970f20 +# input_hash: f9e524a368611b4591c0b79cc851d7fd034bcb935240ad118e3fe4c7b27edeb4 channels: - conda-forge @@ -8,19 +8,19 @@ channels: - nvidia - nodefaults dependencies: - - ca-certificates=2023.5.7=h56e8100_0 + - ca-certificates=2023.7.22=h56e8100_0 - cuda-cccl-impl=2.0.1=h57928b3_0 - cuda-cudart=11.8.89=0 - cuda-cupti=11.8.87=0 - cuda-nvrtc=11.8.89=0 - cuda-nvtx=11.8.86=0 - - cuda-profiler-api=12.2.53=0 + - cuda-profiler-api=12.2.128=0 - cuda-version=12.0=hffde075_2 - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - font-ttf-inconsolata=3.000=h77eed37_0 - font-ttf-source-code-pro=2.038=h77eed37_0 - font-ttf-ubuntu=0.83=hab24e00_0 - - intel-openmp=2023.1.0=h57928b3_46319 + - intel-openmp=2023.2.0=h57928b3_49496 - libcublas=11.11.3.6=0 - libcufft=10.9.0.58=0 - libcusolver=11.4.1.48=0 @@ -62,7 +62,7 @@ dependencies: - cuda-cudart-dev=11.8.89=0 - dav1d=1.2.0=hcfcfb64_0 - double-conversion=3.2.0=h63175ca_1 - - eigen=3.4.1=h91493d7_0 + - eigen=3.4.0=h91493d7_0 - fftw=3.3.10=nompi_h38027f0_108 - fribidi=1.0.10=h8d14728_0 - getopt-win32=0.1=h8ffe710_0 @@ -83,13 +83,13 @@ dependencies: - libopus=1.3.1=h8ffe710_1 - libsodium=1.0.18=h8d14728_1 - libsqlite=3.42.0=hcfcfb64_0 - - libuv=1.44.2=h8ffe710_0 + - libuv=1.44.2=hcfcfb64_1 - libwebp-base=1.3.1=hcfcfb64_0 - libzlib=1.2.13=hcfcfb64_5 - lz4-c=1.9.4=hcfcfb64_0 - m2w64-gcc-libgfortran=5.3.0=6 - openh264=2.3.1=h63175ca_2 - - openssl=3.1.1=hcfcfb64_1 + - openssl=3.1.2=hcfcfb64_0 - pixman=0.40.0=h8ffe710_0 - pthreads-win32=2.9.1=hfa6e2cd_3 - pugixml=1.11.4=h63175ca_1 @@ -105,7 +105,7 @@ dependencies: - krb5=1.20.1=heb0366b_0 - libbrotlidec=1.0.9=hcfcfb64_9 - libbrotlienc=1.0.9=hcfcfb64_9 - - libclang13=15.0.7=default_h77d9078_2 + - libclang13=15.0.7=default_h77d9078_3 - libcurand-dev=10.3.1.50=h63175ca_0 - libpng=1.6.39=h19919ed_0 - libprotobuf=4.23.3=h1975477_0 @@ -124,22 +124,27 @@ dependencies: - zstd=1.5.2=h12be248_7 - absl-py=1.4.0=pyhd8ed1ab_0 - alabaster=0.7.13=pyhd8ed1ab_0 + - appdirs=1.4.4=pyh9f0ad1d_0 - attrs=21.4.0=pyhd8ed1ab_0 - backcall=0.2.0=pyh9f0ad1d_0 - backports=1.0=pyhd8ed1ab_3 - blinker=1.6.2=pyhd8ed1ab_0 + - boltons=23.0.0=pyhd8ed1ab_0 - brotli-bin=1.0.9=hcfcfb64_9 + - cached_property=1.5.2=pyha770c72_1 - cachetools=5.3.1=pyhd8ed1ab_0 - - certifi=2023.5.7=pyhd8ed1ab_0 + - certifi=2023.7.22=pyhd8ed1ab_0 - charset-normalizer=3.2.0=pyhd8ed1ab_0 - colorama=0.4.6=pyhd8ed1ab_0 + - crashtest=0.4.1=pyhd8ed1ab_0 - cuda-libraries-dev=11.8.0=0 - cuda-runtime=11.8.0=0 - cycler=0.11.0=pyhd8ed1ab_0 - dataclasses=0.8=pyhc8e2a94_3 - - debugpy=1.6.7=py310h00ffb61_0 + - debugpy=1.6.8=py310h00ffb61_0 - decorator=5.1.1=pyhd8ed1ab_0 - defusedxml=0.7.1=pyhd8ed1ab_0 + - distlib=0.3.7=pyhd8ed1ab_0 - docutils=0.17.1=py310h5588dad_3 - entrypoints=0.4=pyhd8ed1ab_0 - exceptiongroup=1.1.2=pyhd8ed1ab_0 @@ -157,20 +162,25 @@ dependencies: - iniconfig=2.0.0=pyhd8ed1ab_0 - ipython_genutils=0.2.0=py_1 - jmespath=1.0.1=pyhd8ed1ab_0 + - jsonpointer=2.0=py_0 - jupyterlab_widgets=3.0.8=pyhd8ed1ab_0 - kiwisolver=1.4.4=py310h232114e_1 - lazy-object-proxy=1.9.0=py310h8d17308_0 - - libclang=15.0.7=default_h77d9078_2 + - libclang=15.0.7=default_h77d9078_3 - libcurl=8.1.2=h68f0423_0 - libglib=2.76.4=he8f3873_0 - libgrpc=1.56.2=hea2d5f7_0 - libhwloc=2.9.1=h51c2c0f_0 - libtiff=4.4.0=hc4f729c_5 + - lockfile=0.12.2=py_1 - markupsafe=2.1.3=py310h8d17308_0 - mccabe=0.7.0=pyhd8ed1ab_0 - mdurl=0.1.0=pyhd8ed1ab_0 + - menuinst=1.4.19=py310h5588dad_1 - mistune=3.0.0=pyhd8ed1ab_0 + - more-itertools=10.1.0=pyhd8ed1ab_0 - mpmath=1.3.0=pyhd8ed1ab_0 + - msgpack-python=1.0.5=py310h232114e_0 - multidict=6.0.4=py310h8d17308_0 - munkres=1.1.4=pyh9f0ad1d_0 - mypy_extensions=1.0.0=pyha770c72_0 @@ -179,33 +189,39 @@ dependencies: - packaging=23.1=pyhd8ed1ab_0 - pandocfilters=1.5.0=pyhd8ed1ab_0 - parso=0.8.3=pyhd8ed1ab_0 - - pathspec=0.11.1=pyhd8ed1ab_0 + - pathspec=0.11.2=pyhd8ed1ab_0 - pickleshare=0.7.5=py_1003 + - pkginfo=1.9.6=pyhd8ed1ab_0 - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0 - pluggy=1.2.0=pyhd8ed1ab_0 - ply=3.11=py_1 - prometheus_client=0.17.1=pyhd8ed1ab_0 - psutil=5.9.5=py310h8d17308_0 - pthread-stubs=0.4=hcd874cb_1001 + - ptyprocess=0.7.0=pyhd3deb0d_0 - pure_eval=0.2.2=pyhd8ed1ab_0 - pyasn1=0.4.8=py_0 - pycodestyle=2.10.0=pyhd8ed1ab_0 + - pycosat=0.6.4=py310h8d17308_1 - pycparser=2.21=pyhd8ed1ab_0 - pyflakes=3.0.1=pyhd8ed1ab_0 - pygments=2.15.1=pyhd8ed1ab_0 - pyjwt=2.8.0=pyhd8ed1ab_0 - pyparsing=3.0.9=pyhd8ed1ab_0 - pyrsistent=0.19.3=py310h8d17308_0 - - python-fastjsonschema=2.17.1=pyhd8ed1ab_0 + - python-fastjsonschema=2.18.0=pyhd8ed1ab_0 + - python-installer=0.7.0=pyhd8ed1ab_0 - python-json-logger=2.0.7=pyhd8ed1ab_0 - pytz=2023.3=pyhd8ed1ab_0 - pywin32=304=py310h00ffb61_2 + - pywin32-ctypes=0.2.2=py310h5588dad_0 - pywinpty=2.0.11=py310h00ffb61_0 - pyyaml=6.0=py310h8d17308_5 - pyzmq=25.1.0=py310hcd737a0_0 - rfc3986-validator=0.1.1=pyh9f0ad1d_0 - ruamel.yaml.clib=0.2.7=py310h8d17308_1 - setuptools=67.7.2=pyhd8ed1ab_0 + - shellingham=1.5.1=pyhd8ed1ab_0 - six=1.16.0=pyh6c4a22f_0 - sniffio=1.3.0=pyhd8ed1ab_0 - snowballstemmer=2.2.0=pyhd8ed1ab_0 @@ -220,17 +236,23 @@ dependencies: - tensorboard-data-server=0.7.0=py310h5588dad_0 - toml=0.10.2=pyhd8ed1ab_0 - tomli=2.0.1=pyhd8ed1ab_0 + - tomlkit=0.12.1=pyha770c72_0 + - toolz=0.12.0=pyhd8ed1ab_0 - tornado=6.3.2=py310h8d17308_0 - traitlets=5.9.0=pyhd8ed1ab_0 + - trove-classifiers=2023.7.6=pyhd8ed1ab_0 - typed-ast=1.5.5=py310h8d17308_0 + - typing=3.10.0.0=pyhd8ed1ab_0 - typing_extensions=4.7.1=pyha770c72_0 - typing_utils=0.1.0=pyhd8ed1ab_0 - uc-micro-py=1.0.1=pyhd8ed1ab_0 - unicodedata2=15.0.0=py310h8d17308_0 - unidecode=1.3.6=pyhd8ed1ab_0 + - uri-template=1.3.0=pyhd8ed1ab_0 + - webcolors=1.13=pyhd8ed1ab_0 - webencodings=0.5.1=py_1 - websocket-client=1.6.1=pyhd8ed1ab_0 - - wheel=0.40.0=pyhd8ed1ab_1 + - wheel=0.41.0=pyhd8ed1ab_0 - widgetsnbextension=4.0.8=pyhd8ed1ab_0 - win32_setctime=1.1.0=pyhd8ed1ab_0 - win_inet_pton=1.1.0=pyhd8ed1ab_6 @@ -247,13 +269,15 @@ dependencies: - anyio=3.7.1=pyhd8ed1ab_0 - asttokens=2.2.1=pyhd8ed1ab_0 - babel=2.12.1=pyhd8ed1ab_1 + - backports.cached-property=1.0.2=pyhd8ed1ab_0 - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0 - beautifulsoup4=4.12.2=pyha770c72_0 - bleach=6.0.0=pyhd8ed1ab_0 - brotli=1.0.9=hcfcfb64_9 + - cached-property=1.5.2=hd8ed1ab_1 - cffi=1.15.1=py310h628cb3f_3 - click=8.1.6=win_pyh7428d3b_0 - - comm=0.1.3=pyhd8ed1ab_0 + - comm=0.1.4=pyhd8ed1ab_0 - curl=8.1.2=h68f0423_0 - dacite=1.8.0=pyhd8ed1ab_0 - deprecation=2.1.0=pyh9f0ad1d_0 @@ -263,10 +287,13 @@ dependencies: - grpcio=1.56.2=py310hb84602e_0 - gts=0.7.6=h6b5321d_4 - hdf5=1.12.2=nompi_h57737ce_101 + - html5lib=1.1=pyh9f0ad1d_0 - importlib-metadata=6.8.0=pyha770c72_0 - importlib_resources=6.0.0=pyhd8ed1ab_1 - - jedi=0.18.2=pyhd8ed1ab_0 + - jaraco.classes=3.3.0=pyhd8ed1ab_0 + - jedi=0.19.0=pyhd8ed1ab_0 - jinja2=3.1.2=pyhd8ed1ab_1 + - jsonpatch=1.32=pyhd8ed1ab_0 - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 - latexcodec=2.0.1=pyh9f0ad1d_0 - lcms2=2.14=h90d422f_0 @@ -278,6 +305,7 @@ dependencies: - matplotlib-inline=0.1.6=pyhd8ed1ab_0 - openjpeg=2.5.0=hc9384bd_1 - overrides=7.3.1=pyhd8ed1ab_0 + - pexpect=4.8.0=pyh1a96a4e_2 - pip=23.1.2=pyhd8ed1ab_0 - proj=9.1.0=h3863b3b_0 - protobuf=4.23.3=py310ha3d488f_0 @@ -293,7 +321,7 @@ dependencies: - rsa=4.9=pyhd8ed1ab_0 - ruamel.yaml=0.17.32=py310h8d17308_0 - send2trash=1.8.2=pyh08f2357_0 - - sip=6.7.9=py310h00ffb61_0 + - sip=6.7.11=py310h00ffb61_0 - sympy=1.12=pyh04b8f61_3 - tbb=2021.9.0=h91493d7_0 - terminado=0.17.0=pyh08f2357_0 @@ -303,14 +331,18 @@ dependencies: - werkzeug=2.3.6=pyhd8ed1ab_0 - xorg-libsm=1.2.3=hcd874cb_1000 - yarl=1.9.2=py310h8d17308_0 + - annotated-types=0.5.0=pyhd8ed1ab_0 - argon2-cffi-bindings=21.2.0=py310h8d17308_3 + - arrow=1.2.3=pyhd8ed1ab_0 - astroid=2.15.6=py310h5588dad_0 - async-timeout=4.0.2=pyhd8ed1ab_0 - brotlipy=0.7.0=py310h8d17308_1005 - cairo=1.16.0=hd694305_1014 + - click-default-group=1.2.2=pyhd8ed1ab_1 - cryptography=41.0.2=py310h6e82f81_0 - ffmpeg=5.1.2=gpl_h5037a79_109 - - fonttools=4.41.0=py310h8d17308_0 + - fonttools=4.42.0=py310h8d17308_0 + - fqdn=1.5.1=pyhd8ed1ab_0 - ghp-import=2.1.0=pyhd8ed1ab_0 - glib=2.76.4=h12be248_0 - importlib_metadata=6.8.0=hd8ed1ab_0 @@ -318,13 +350,15 @@ dependencies: - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1 - libitk=5.3.0=h6e1890f_0 - libnetcdf=4.8.1=nompi_h8c042bf_106 - - markdown=3.4.3=pyhd8ed1ab_0 + - markdown=3.4.4=pyhd8ed1ab_0 - mdit-py-plugins=0.4.0=pyhd8ed1ab_0 - mkl=2022.1.0=h6a75c08_874 - pillow=9.2.0=py310hd4fb230_3 - - platformdirs=3.9.1=pyhd8ed1ab_0 + - platformdirs=3.10.0=pyhd8ed1ab_0 + - poetry-core=1.6.1=pyhd8ed1ab_0 - pybtex=0.24.0=pyhd8ed1ab_2 - - pyqt5-sip=12.11.0=py310h00ffb61_3 + - pydantic-core=2.4.0=py310h87d50f1_0 + - pyqt5-sip=12.12.2=py310h00ffb61_4 - python-build=0.10.0=pyhd8ed1ab_1 - setuptools-scm=7.1.0=pyhd8ed1ab_0 - sqlalchemy=2.0.19=py310h8d17308_0 @@ -332,65 +366,83 @@ dependencies: - tbb-devel=2021.9.0=h91493d7_0 - wcwidth=0.2.6=pyhd8ed1ab_0 - xorg-libx11=1.8.4=hcd874cb_0 + - zstandard=0.19.0=py310h0009e47_2 - aiohttp=3.8.5=py310h8d17308_0 - argon2-cffi=21.3.0=pyhd8ed1ab_0 - black=22.3.0=pyhd8ed1ab_0 - - gstreamer=1.22.4=hb4038d2_1 + - conda-package-streaming=0.9.0=pyhd8ed1ab_0 + - gstreamer=1.22.5=hb4038d2_0 - harfbuzz=6.0.0=he256f1b_0 + - isoduration=20.11.0=pyhd8ed1ab_0 - jupyter_core=5.3.1=py310h5588dad_0 - - jupyter_events=0.6.3=pyhd8ed1ab_0 + - keyring=23.13.1=py310h5588dad_0 - libblas=3.9.0=17_win64_mkl - mkl-devel=2022.1.0=h57928b3_875 - oauthlib=3.2.2=pyhd8ed1ab_0 + - poetry-plugin-export=1.4.0=pyhd8ed1ab_0 - prompt-toolkit=3.0.39=pyha770c72_0 - pybtex-docutils=1.0.2=py310h5588dad_2 + - pydantic=2.1.1=pyhd8ed1ab_0 - pyopenssl=23.2.0=pyhd8ed1ab_1 - simpleitk=2.2.1=py310hcf936e6_1 + - virtualenv=20.24.2=pyhd8ed1ab_0 - xorg-libxext=1.3.4=hcd874cb_2 - xorg-libxt=1.3.0=hcd874cb_0 + - conda-package-handling=2.2.0=pyh38be061_0 - flake8-black=0.3.6=pyhd8ed1ab_0 - - gst-plugins-base=1.22.4=h001b923_1 + - gst-plugins-base=1.22.5=h001b923_0 + - jsonschema-with-format-nongpl=4.17.3=pyhd8ed1ab_0 - jupyter_client=8.3.0=pyhd8ed1ab_0 - libcblas=3.9.0=17_win64_mkl - liblapack=3.9.0=17_win64_mkl - - nbformat=5.9.1=pyhd8ed1ab_0 + - nbformat=5.9.2=pyhd8ed1ab_0 - pango=1.50.14=hdffb7b3_0 - prompt_toolkit=3.0.39=hd8ed1ab_0 - urllib3=1.26.15=pyhd8ed1ab_0 - wslink=1.11.1=pyhd8ed1ab_0 - xorg-libxpm=3.5.16=hcd874cb_0 - botocore=1.29.165=pyhd8ed1ab_0 + - dulwich=0.21.5=py310h8d17308_0 - ipython=8.14.0=pyh08f2357_0 + - jupyter_events=0.7.0=pyhd8ed1ab_0 - libgd=2.3.3=h891f43f_3 - liblapacke=3.9.0=17_win64_mkl - nbclient=0.7.4=pyhd8ed1ab_0 - - numpy=1.25.1=py310hd02465a_0 + - numpy=1.25.2=py310hd02465a_0 - qt-main=5.15.8=h720456b_6 - requests=2.31.0=pyhd8ed1ab_0 - blas-devel=3.9.0=17_win64_mkl + - cachecontrol=0.12.14=pyhd8ed1ab_0 + - conda=23.7.2=py310h5588dad_0 - contourpy=1.1.0=py310h232114e_0 + - ensureconda=1.4.3=pyhd8ed1ab_0 - google-auth=2.22.0=pyh1a96a4e_0 - graphviz=7.0.6=h51cb2cd_0 - ipykernel=6.23.3=pyh6817e22_0 + - ipywidgets=8.1.0=pyhd8ed1ab_0 - jupyter-cache=0.6.1=pyhd8ed1ab_0 - - nbconvert-core=7.7.1=pyhd8ed1ab_1 + - nbconvert-core=7.7.3=pyhd8ed1ab_0 - nibabel=5.1.0=py310h5588dad_2 - pandas=1.5.3=py310h1c4a608_1 - pooch=1.7.0=pyha770c72_3 - - pyqt=5.15.7=py310h1fd54f2_3 + - pyqt=5.15.9=py310h1fd54f2_4 + - rapidfuzz=2.15.1=py310h00ffb61_0 - requests-oauthlib=1.3.1=pyhd8ed1ab_0 + - requests-toolbelt=1.0.0=pyhd8ed1ab_0 - s3transfer=0.6.1=pyhd8ed1ab_0 - sphinx=4.5.0=pyh6c4a22f_0 - vtk=9.2.5=qt_py310h2fd250f_200 - blas=2.117=mkl - boto3=1.26.165=pyhd8ed1ab_0 + - cachecontrol-with-filecache=0.12.14=pyhd8ed1ab_0 + - cleo=2.0.1=pyhd8ed1ab_0 + - conda-devenv=2.3.0=pyhd8ed1ab_0 - google-auth-oauthlib=1.0.0=pyhd8ed1ab_1 - - ipywidgets=8.0.7=pyhd8ed1ab_0 - jupyter_console=6.6.3=pyhd8ed1ab_0 - jupyter_server=2.7.0=pyhd8ed1ab_0 - matplotlib-base=3.7.2=py310h51140c5_0 - myst-parser=0.18.1=pyhd8ed1ab_0 - - nbconvert-pandoc=7.7.1=pyhd8ed1ab_1 + - nbconvert-pandoc=7.7.3=pyhd8ed1ab_0 - pydata-sphinx-theme=0.13.3=pyhd8ed1ab_0 - qtconsole-base=5.4.3=pyha770c72_0 - scipy=1.10.1=py310h578b7cb_3 @@ -409,19 +461,21 @@ dependencies: - sphinxcontrib-jquery=4.1=pyhd8ed1ab_0 - matplotlib=3.7.2=py310h5588dad_0 - myst-nb=0.17.2=pyhd8ed1ab_0 - - nbconvert=7.7.1=pyhd8ed1ab_1 + - nbconvert=7.7.3=pyhd8ed1ab_0 - notebook-shim=0.2.3=pyhd8ed1ab_0 + - poetry=1.5.1=win_pyhd8ed1ab_0 - pytorch=2.0.1=py3.10_cuda11.8_cudnn8_0 - qtconsole=5.4.3=pyhd8ed1ab_0 - sphinx-autoapi=2.1.0=pyhd8ed1ab_0 - sphinx-book-theme=1.0.1=pyhd8ed1ab_0 - sphinx_rtd_theme=1.2.2=pyha770c72_0 - tensorboard=2.13.0=pyhd8ed1ab_0 + - conda-lock=1.0.5=pyhd8ed1ab_1 - jupyter-book=0.15.1=pyhd8ed1ab_0 - nbclassic=1.0.0=pyhb4ecaf3_1 - torchinfo=1.8.0=pyhd8ed1ab_0 - torchmetrics=0.11.4=pyhd8ed1ab_0 - torchvision=0.15.2=py310_cu118 - notebook=6.5.4=pyha770c72_0 - - pytorch-lightning=2.0.4=pyhd8ed1ab_0 + - pytorch-lightning=2.0.6=pyhd8ed1ab_0 - jupyter=1.0.0=py310h5588dad_8 diff --git a/examples/ffd/register.py b/examples/ffd/register.py index 735e3a8..26eb007 100644 --- a/examples/ffd/register.py +++ b/examples/ffd/register.py @@ -4,20 +4,17 @@ from pathlib import Path import sys from timeit import default_timer as timer -from typing import Any, Dict - -import json -import yaml import torch import torch.cuda from torch import Tensor from deepali.core.argparse import ArgumentParser, Args, main_func +from deepali.core.config import read_config_dict from deepali.core.environ import cuda_visible_devices from deepali.core.grid import Grid from deepali.core.logging import configure_logging -from deepali.core.pathlib import PathStr, unlink_or_mkdir +from deepali.core.pathlib import unlink_or_mkdir from deepali.data import Image from deepali.modules import TransformImage @@ -103,7 +100,7 @@ def init(args: Args) -> int: def func(args: Args) -> int: r"""Execute registration given parsed arguments.""" - config = load_config(args.config) + config = read_config_dict(args.config) device = torch.device("cuda:0" if args.device == "cuda" else "cpu") start = timer() transform = register_pairwise( @@ -153,15 +150,5 @@ def func(args: Args) -> int: main = main_func(parser, func, init=init) -def load_config(path: PathStr) -> Dict[str, Any]: - r"""Load registration parameters from configuration file.""" - config_path = Path(path).absolute() - log.info(f"Load configuration from {config_path}") - config_text = config_path.read_text() - if config_path.suffix == ".json": - return json.loads(config_text) - return yaml.safe_load(config_text) - - if __name__ == "__main__": sys.exit(main()) diff --git a/pyproject.toml b/pyproject.toml index a75a651..0662ff2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,7 +41,6 @@ dependencies = [ "dacite", "deprecation", "pandas", - "pyyaml", "ruamel.yaml", "torch>=1.9", "typing-extensions", diff --git a/src/deepali/core/__init__.py b/src/deepali/core/__init__.py index 8ada512..ec3eabd 100644 --- a/src/deepali/core/__init__.py +++ b/src/deepali/core/__init__.py @@ -30,6 +30,10 @@ from .grid import grid_transform_points from .grid import grid_transform_vectors +from .pathlib import is_uri +from .pathlib import to_uri +from .storage import StorageObject + from .typing import Array from .typing import Batch from .typing import Dataclass @@ -86,6 +90,7 @@ "ScalarOrTuple3d", "Size", "Shape", + "StorageObject", "TensorCollection", "grid_points_transform", "grid_vectors_transform", @@ -97,4 +102,6 @@ "is_uint_dtype", "is_namedtuple", "is_path_str", + "is_uri", + "to_uri", ) diff --git a/src/deepali/core/config.py b/src/deepali/core/config.py index 52d44a6..eb918b7 100644 --- a/src/deepali/core/config.py +++ b/src/deepali/core/config.py @@ -3,7 +3,7 @@ from __future__ import annotations from dataclasses import asdict, fields -from pathlib import Path +from io import StringIO from typing import Any, Dict, Mapping, Optional, Sequence, TypeVar, Type import dacite @@ -13,7 +13,8 @@ # (cf. https://github.com/iterative/dvc/issues/8466#issuecomment-1290757564) from ruamel.yaml import YAML -from .pathlib import PathStr, abspath_template +from .pathlib import Path, PathUri, abspath_template +from .storage import StorageObject from .typing import is_path_str_field @@ -42,18 +43,9 @@ def from_dict(cls: Type[T], arg: Mapping[str, Any], parent: Optional[Path] = Non return config @classmethod - def from_path(cls: Type[T], path: PathStr, section: Optional[str] = None) -> T: + def from_path(cls: Type[T], path: PathUri, section: Optional[str] = None) -> T: r"""Load configuration from file.""" - path = Path(path).absolute() - if path.suffix not in (".json", ".yaml", ".yml"): - raise ValueError(f"{cls.__name__}.write() 'path' has unsupported suffix {path.suffix}") - with path.open("rt") as fp: - if path.suffix == ".json": - config = json.load(fp) - else: - config = YAML(typ="safe").load(fp) - if config is None: - config = {} + config = read_config_dict(path) if section is None: section = cls.section() if section: @@ -62,24 +54,14 @@ def from_path(cls: Type[T], path: PathStr, section: Optional[str] = None) -> T: return cls.from_dict(config, parent=path.parent) @classmethod - def read(cls: Type[T], path: PathStr, section: Optional[str] = None) -> T: - r"""Load configuration from file.""" + def read(cls: Type[T], path: PathUri, section: Optional[str] = None) -> T: + r"""Load configuration from JSON or YAML file.""" return cls.from_path(path, section=section) - def write(self, path: PathStr) -> None: - r"""Write configuration to file.""" + def write(self, path: PathUri) -> None: + r"""Save configuration to JSON or YAML file.""" config = self.asdict() - path = Path(path).absolute() - if path.suffix not in (".json", ".yaml", ".yml"): - raise ValueError( - f"{type(self).__name__}.write() 'path' has unsupported suffix {path.suffix}" - ) - path.parent.mkdir(parents=True, exist_ok=True) - with path.open("wt") as fp: - if path.suffix == ".json": - json.dump(config, fp) - else: - YAML(typ="safe").dump(config, fp) + write_config_dict(config, path) def asdict(self) -> Dict[str, Any]: r"""Get configuration dictionary.""" @@ -184,3 +166,34 @@ def join_kwargs_in_sequence(arg): kwargs[name] = value arg = kwargs if start == 0 else (arg[0], kwargs) return arg + + +def read_config_dict(path: PathUri) -> Dict[str, Any]: + r"""Read configuration from JSON or YAML file.""" + with StorageObject.from_path(path) as config_object: + config_suffix = config_object.path.suffix + if config_suffix.lower() not in (".json", ".yaml", ".yml"): + raise ValueError(f"read_config_dict() 'path' has unsupported suffix {config_suffix}") + config_text = config_object.read_text() + if config_suffix == ".json": + config_dict = json.loads(config_text) + else: + config_dict = YAML(typ="safe").load(config_text) + if config_dict is None: + config_dict = {} + return config_dict + + +def write_config_dict(config: Dict[str, Any], path: PathUri) -> None: + r"""Write configuration to JSON or YAML file.""" + with StorageObject.from_path(path) as config_object: + config_suffix = config_object.path.suffix + if config_suffix.lower() not in (".json", ".yaml", ".yml"): + raise ValueError(f"write_config_dict() 'path' has unsupported suffix {config_suffix}") + if config_suffix == ".json": + config_text = json.dumps(config) + "\n" + else: + buffer = StringIO() + YAML(typ="safe").dump(config, buffer) + config_text = buffer.getvalue() + config_object.write_text(config_text) diff --git a/src/deepali/utils/storage.py b/src/deepali/core/storage.py similarity index 97% rename from src/deepali/utils/storage.py rename to src/deepali/core/storage.py index 54bb701..681bf12 100644 --- a/src/deepali/utils/storage.py +++ b/src/deepali/core/storage.py @@ -9,7 +9,7 @@ from typing import Generator, Optional, TypeVar, cast from urllib.parse import urlsplit -from deepali.core.pathlib import PathStr, PathUri, to_uri, unlink_or_mkdir +from .pathlib import PathStr, PathUri, to_uri, unlink_or_mkdir __all__ = ( @@ -145,8 +145,10 @@ def from_uri(uri: str) -> StorageObject: return LocalObject(Path("/" + res.netloc + "/" + path if res.netloc else path)) if res.scheme == "s3": # DO NOT import at module level to avoid cyclical import! - from .aws.s3.object import S3Object - + try: + from deepali.utils.aws.s3.object import S3Object + except ImportError: + raise ImportError("StorageObject.from_uri() requires AWS S3 deepali[utils]") return cast(StorageObject, S3Object.from_uri(uri)) raise ValueError("Invalid or unsupported storage object URI: %s", uri) diff --git a/src/deepali/spatial/nonrigid.py b/src/deepali/spatial/nonrigid.py index a4cc655..9f45411 100644 --- a/src/deepali/spatial/nonrigid.py +++ b/src/deepali/spatial/nonrigid.py @@ -161,7 +161,7 @@ def fit(self, flow: FlowFields, **kwargs) -> DisplacementFieldTransform: grid = self.grid().resize(self.data_shape[:1:-1]) flow = flow.to(self.device) flow = flow.sample(grid) - flow = flow.axes(Axes.from_grid(grid)) + flow = flow.axes(grid.axes()) if callable(params): self._fit(flow, **kwargs) else: diff --git a/src/deepali/utils/aws/s3/object.py b/src/deepali/utils/aws/s3/object.py index eadaadc..60d6b1c 100644 --- a/src/deepali/utils/aws/s3/object.py +++ b/src/deepali/utils/aws/s3/object.py @@ -10,7 +10,7 @@ from typing import Generator, Optional from deepali.core.pathlib import PathStr, to_uri -from deepali.utils.storage import StorageObject +from deepali.core.storage import StorageObject from .client import S3Client diff --git a/src/deepali/utils/imageio/meta.py b/src/deepali/utils/imageio/meta.py index 260874c..68df4a4 100644 --- a/src/deepali/utils/imageio/meta.py +++ b/src/deepali/utils/imageio/meta.py @@ -11,7 +11,7 @@ from deepali.core.grid import Grid from deepali.core.pathlib import PathUri, path_suffix -from deepali.utils.storage import StorageObject +from deepali.core.storage import StorageObject META_IMAGE_SUFFIXES = (".mha", ".mhd") diff --git a/src/deepali/utils/imageio/nifti.py b/src/deepali/utils/imageio/nifti.py index f821809..d836ce8 100644 --- a/src/deepali/utils/imageio/nifti.py +++ b/src/deepali/utils/imageio/nifti.py @@ -14,7 +14,7 @@ from deepali.core.grid import Grid from deepali.core.pathlib import PathUri, path_suffix, unlink_or_mkdir -from deepali.utils.storage import StorageObject +from deepali.core.storage import StorageObject NIFTI_IMAGE_SUFFIXES = (".nia", ".nii", ".nii.gz", ".hdr", ".hdr.gz", ".img", ".img.gz") diff --git a/src/deepali/utils/simpleitk/imageio.py b/src/deepali/utils/simpleitk/imageio.py index 620c3f9..078048a 100644 --- a/src/deepali/utils/simpleitk/imageio.py +++ b/src/deepali/utils/simpleitk/imageio.py @@ -1,5 +1,5 @@ from deepali.core.pathlib import PathUri, unlink_or_mkdir -from deepali.utils.storage import StorageObject +from deepali.core.storage import StorageObject import SimpleITK as sitk diff --git a/src/deepali/utils/vtk/polydataio.py b/src/deepali/utils/vtk/polydataio.py index dcb07f3..ad01c53 100644 --- a/src/deepali/utils/vtk/polydataio.py +++ b/src/deepali/utils/vtk/polydataio.py @@ -12,7 +12,7 @@ from vtk import vtkPolyDataReader, vtkPolyDataWriter from deepali.core.pathlib import PathUri -from deepali.utils.storage import StorageObject +from deepali.core.storage import StorageObject from .numpy import vtk_to_numpy_array, vtk_to_numpy_points