mirror of
https://github.com/SebastianWendel/nixpkgs.git
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Merge pull request #156027 from simeoncarstens/fix-tfp
This commit is contained in:
Sandro
GitHub
commit
cfeee25aa9
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@ -9,11 +9,14 @@
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, numpy
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, pandas
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, pytest
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, cloudpickle
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, scipy
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, setuptools
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, tensorflow-probability
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, typing-extensions
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# , tensorflow-probability (incompatible version)
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, xarray
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#, h5py (used by disabled tests)
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, zarr
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, h5py
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#, pymc3 (broken)
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#, pyro-ppl (broken)
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#, pystan (not packaged)
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@ -45,28 +48,36 @@ buildPythonPackage rec {
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scipy
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];
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postPatch = ''
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substituteInPlace requirements.txt \
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--replace "typing_extensions>=3.7.4.3,<4" "typing_extensions>=3.7.4.3"
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'';
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checkInputs = [
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bokeh
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emcee
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numba
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pytest
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tensorflow-probability
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#h5py (used by disabled tests)
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#pymc3 (broken)
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#pyro-ppl (broken)
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cloudpickle
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zarr
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#tensorflow-probability (used by disabled tests)
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h5py
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#pymc3 (broken, used by disabled tests)
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#pyro-ppl (broken, used by disabled tests)
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#pystan (not packaged)
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#numpyro (not packaged)
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#numpyro (not packaged, used by disabled tests)
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];
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# check requires pymc3 and pyro-ppl, which are currently broken, and pystan
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# and numpyro, which are not yet packaged, some checks also need to make
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# and numpyro, which are not yet packaged, and an incompatible (old) version
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# of tensorflow-probability. some checks also need to make
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# directories and do not have permission to do so. So we can only check part
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# of the package
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# Additionally, there are some failures with the plots test, which revolve
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# around attempting to output .mp4 files through an interface that only wants
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# to output .html files.
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# The following test have been disabled as a result: data_cmdstanpy,
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# data_numpyro, data_pyro, data_pystan, and plots.
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# data_numpyro, data_pyro, data_pystan, data_tfp, data_pymc3 and plots.
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checkPhase = ''
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cd arviz/tests/
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export HOME=$TMPDIR
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@ -76,11 +87,13 @@ buildPythonPackage rec {
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base_tests/test_plot_utils.py \
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base_tests/test_rcparams.py \
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base_tests/test_stats.py \
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base_tests/test_stats_numba.py \
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base_tests/test_stats_utils.py \
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base_tests/test_utils.py \
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base_tests/test_utils_numba.py \
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base_tests/test_data_zarr.py \
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external_tests/test_data_cmdstan.py \
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external_tests/test_data_emcee.py \
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external_tests/test_data_tfp.py
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external_tests/test_data_emcee.py
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'';
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meta = with lib; {
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@ -86,5 +86,6 @@ in buildPythonPackage {
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license = licenses.asl20;
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maintainers = with maintainers; [ timokau ];
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platforms = platforms.linux;
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broken = true; # depends on older TensorFlow version than is currently packaged
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};
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}
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@ -68,5 +68,8 @@ buildPythonPackage rec {
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homepage = "https://github.com/pymc-devs/pymc3";
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license = lib.licenses.asl20;
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maintainers = with lib.maintainers; [ ilya-kolpakov ];
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# several dependencies are not declared and in the end it requires theano-pymc3
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# instead of Theano. The former is currently not packaged.
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broken = true;
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};
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}
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@ -1,7 +1,5 @@
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{ lib
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, fetchFromGitHub
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, fetchpatch
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, bazel_0_26
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, buildBazelPackage
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, buildPythonPackage
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, python
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@ -11,47 +9,33 @@
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, tensorflow
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, six
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, numpy
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, dm-tree
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, keras
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, decorator
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, cloudpickle
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, gast
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, hypothesis
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, scipy
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, pandas
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, mpmath
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, matplotlib
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, mock
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, pytest
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}:
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let
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version = "0.8.0";
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version = "0.15.0";
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pname = "tensorflow_probability";
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# first build all binaries and generate setup.py using bazel
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bazel-wheel = buildBazelPackage {
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bazel = bazel_0_26;
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name = "${pname}-${version}-py2.py3-none-any.whl";
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src = fetchFromGitHub {
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owner = "tensorflow";
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repo = "probability";
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rev = version;
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sha256 = "07cm8zba8n0ihzdm3k4a4rsg5v62xxsfvcw4h0niz91c0parqjqy";
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rev = "v" + version;
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sha256 = "155fgmra90s08vjnp61qxdrpzq74xa3kdzhgdkavwgc25pvxn3mi";
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};
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patches = [
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(fetchpatch {
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name = "gast-0.3.patch";
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url = "https://github.com/tensorflow/probability/commit/ae7a9d9771771ec1e7755a3588b9325f050a84cc.patch";
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sha256 = "0kfhx30gshm8f3945na9yjjik71r20qmjzifbigaj4l8dwd9dz1a";
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excludes = ["testing/*"];
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})
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(fetchpatch {
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name = "cloudpickle-1.2.patch";
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url = "https://github.com/tensorflow/probability/commit/78ef12b5afe3f567d16c70b74015ed1ddff1b0c8.patch";
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sha256 = "12ms2xcljvvrnig0j78s3wfv4yf3bm5ps4rgfgv5lg2a8mzpc1ga";
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})
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];
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nativeBuildInputs = [
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# needed to create the output wheel in installPhase
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python
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bazelTarget = ":pip_pkg";
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fetchAttrs = {
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sha256 = "1qw7vkwnxy45z4vm94isq5m96xiz35sigag7vjg1xb2sklbymxh8";
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sha256 = "0sgxdlw5x3dydy53l10vbrj8smh78b7r1wff8jxcgp4w69mk8zfm";
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};
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buildAttrs = {
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@ -98,34 +82,31 @@ in buildPythonPackage {
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decorator
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cloudpickle
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gast
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dm-tree
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keras
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];
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# Listed here:
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# https://github.com/tensorflow/probability/blob/f01d27a6f256430f03b14beb14d37def726cb257/testing/run_tests.sh#L58
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# https://github.com/tensorflow/probability/blob/f3777158691787d3658b5e80883fe1a933d48989/testing/dependency_install_lib.sh#L83
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checkInputs = [
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hypothesis
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pytest
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scipy
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pandas
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mpmath
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matplotlib
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mock
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];
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# actual checks currently fail because for some reason
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# tf.enable_eager_execution is called too late. Probably because upstream
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# intents these tests to be run by bazel, not plain pytest.
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# checkPhase = ''
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# # tests need to import from other test files
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# export PYTHONPATH="$PWD/tensorflow-probability:$PYTHONPATH"
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# py.test
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# '';
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# Ideally, we run unit tests with pytest, but in checkPhase, only the Bazel-build wheel is available.
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# But it seems not guaranteed that running the tests with pytest will even work, see
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# https://github.com/tensorflow/probability/blob/c2a10877feb2c4c06a4dc58281e69c37a11315b9/CONTRIBUTING.md?plain=1#L69
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# Ideally, tests would be run using Bazel. For now, lets's do a...
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# sanity check
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checkPhase = ''
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python -c 'import tensorflow_probability'
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'';
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pythonImportsCheck = [ "tensorflow_probability" ];
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meta = with lib; {
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broken = true; # tf-probability 0.8.0 is not compatible with tensorflow 2.3.2
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description = "Library for probabilistic reasoning and statistical analysis";
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homepage = "https://www.tensorflow.org/probability/";
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license = licenses.asl20;
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@ -2,6 +2,7 @@
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, fetchPypi
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, buildPythonPackage
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, pythonOlder
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, pythonAtLeast
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, numpy
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, wheel
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, werkzeug
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@ -24,7 +25,7 @@ buildPythonPackage rec {
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pname = "tensorflow-tensorboard";
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version = "2.6.0";
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format = "wheel";
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disabled = pythonOlder "3.6";
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disabled = pythonOlder "3.6" || pythonAtLeast "3.10";
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src = fetchPypi {
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pname = "tensorboard";
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