diff options
Diffstat (limited to 'pkgs/development/python-modules')
10 files changed, 251 insertions, 94 deletions
diff --git a/pkgs/development/python-modules/aiosomecomfort/default.nix b/pkgs/development/python-modules/aiosomecomfort/default.nix index e993813081a85..5775aece8060b 100644 --- a/pkgs/development/python-modules/aiosomecomfort/default.nix +++ b/pkgs/development/python-modules/aiosomecomfort/default.nix @@ -1,15 +1,16 @@ { lib +, aiohttp , buildPythonPackage , fetchFromGitHub -, aiohttp , prettytable , pythonOlder +, setuptools }: buildPythonPackage rec { pname = "aiosomecomfort"; - version = "0.0.17"; - format = "setuptools"; + version = "0.0.22"; + pyproject = true; disabled = pythonOlder "3.7"; @@ -17,9 +18,13 @@ buildPythonPackage rec { owner = "mkmer"; repo = "AIOSomecomfort"; rev = "refs/tags/${version}"; - hash = "sha256-HJbLsl1NHZxfH17mIi0T6h5ZSfKaw4VYbNgN6vmN7l4="; + hash = "sha256-d4pyt9+sBPNo/PL05HQ4sjyjubMtTZI9WUGRU1B/dH0="; }; + nativeBuildInputs = [ + setuptools + ]; + propagatedBuildInputs = [ aiohttp prettytable @@ -29,7 +34,8 @@ buildPythonPackage rec { "aiosomecomfort" ]; - doCheck = false; # tests only run on windows, due to WindowsSelectorEventLoopPolicy + # Tests only run on Windows, due to WindowsSelectorEventLoopPolicy + doCheck = false; meta = { description = "AsyicIO client for US models of Honeywell Thermostats"; diff --git a/pkgs/development/python-modules/deap/default.nix b/pkgs/development/python-modules/deap/default.nix index 4f0d493c0f80c..ad69642a4f7bb 100644 --- a/pkgs/development/python-modules/deap/default.nix +++ b/pkgs/development/python-modules/deap/default.nix @@ -1,4 +1,10 @@ -{ lib, buildPythonPackage, fetchPypi, numpy, matplotlib, nose }: +{ lib +, buildPythonPackage +, fetchPypi +, matplotlib +, numpy +, pytestCheckHook +}: buildPythonPackage rec { pname = "deap"; @@ -9,19 +15,13 @@ buildPythonPackage rec { hash = "sha256-zAHemJLfp9G8mAPasoiS/q0XfwGCyB20c2CiQOrXeP8="; }; - propagatedBuildInputs = [ numpy matplotlib ]; - - nativeCheckInputs = [ nose ]; - checkPhase = '' - nosetests --verbosity=3 - ''; + propagatedBuildInputs = [ matplotlib numpy ]; + nativeCheckInputs = [ pytestCheckHook ]; meta = with lib; { - description = "DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas."; + description = "A novel evolutionary computation framework for rapid prototyping and testing of ideas"; homepage = "https://github.com/DEAP/deap"; - license = licenses.lgpl3; - maintainers = with maintainers; [ psyanticy ]; + license = licenses.lgpl3Plus; + maintainers = with maintainers; [ getpsyched psyanticy ]; }; - } - diff --git a/pkgs/development/python-modules/glueviz/default.nix b/pkgs/development/python-modules/glueviz/default.nix index c6fb2859b413c..2d0e927c1acc4 100644 --- a/pkgs/development/python-modules/glueviz/default.nix +++ b/pkgs/development/python-modules/glueviz/default.nix @@ -29,7 +29,7 @@ buildPythonPackage rec { pname = "glueviz"; - version = "1.14.1"; + version = "1.16.0"; disabled = pythonOlder "3.7"; @@ -37,7 +37,7 @@ buildPythonPackage rec { owner = "glue-viz"; repo = "glue"; rev = "refs/tags/v${version}"; - sha256 = "sha256-pHUcvyDziE7l0foEz7cygMuAwggnIWzsQy9SFZCDkXA="; + sha256 = "sha256-jjDa0DxB5AJm+x8P7FiH2kqhhc/bbzjzvdC9INs69Ro="; }; buildInputs = [ pyqt-builder ]; diff --git a/pkgs/development/python-modules/httpx-auth/default.nix b/pkgs/development/python-modules/httpx-auth/default.nix new file mode 100644 index 0000000000000..5c099d91d436f --- /dev/null +++ b/pkgs/development/python-modules/httpx-auth/default.nix @@ -0,0 +1,55 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, pythonOlder +, setuptools +, setuptools-scm +, wheel +, httpx +, pyjwt +, pytest-httpx +, pytestCheckHook +}: + +buildPythonPackage rec { + pname = "httpx-auth"; + version = "0.18.0"; + pyproject = true; + + disabled = pythonOlder "3.9"; + + src = fetchFromGitHub { + owner = "Colin-b"; + repo = "httpx_auth"; + rev = "refs/tags/v${version}"; + hash = "sha256-kK31jpS9Ax5kNkvUSbWWIC6CKdZKVJ28kLS0iuntWqg="; + }; + + nativeBuildInputs = [ + setuptools + setuptools-scm + wheel + ]; + + propagatedBuildInputs = [ + httpx + ]; + + nativeCheckInputs = [ + pyjwt + pytest-httpx + pytestCheckHook + ]; + + pythonImportsCheck = [ "httpx_auth" ]; + + __darwinAllowLocalNetworking = true; + + meta = with lib; { + description = "Authentication classes to be used with httpx"; + homepage = "https://github.com/Colin-b/httpx_auth"; + changelog = "https://github.com/Colin-b/httpx_auth/blob/${src.rev}/CHANGELOG.md"; + license = licenses.mit; + maintainers = with maintainers; [ natsukium ]; + }; +} diff --git a/pkgs/development/python-modules/jupyterlab-git/default.nix b/pkgs/development/python-modules/jupyterlab-git/default.nix index 7c0522c754016..fc534f9e67f61 100644 --- a/pkgs/development/python-modules/jupyterlab-git/default.nix +++ b/pkgs/development/python-modules/jupyterlab-git/default.nix @@ -1,34 +1,41 @@ { lib -, stdenv , buildPythonPackage , fetchPypi , git , jupyter-server -, jupyter-packaging +, hatch-jupyter-builder +, hatch-nodejs-version +, hatchling , jupyterlab , nbdime , nbformat , pexpect , pytest-asyncio +, pytest-jupyter , pytest-tornasync , pytestCheckHook , pythonOlder +, traitlets }: buildPythonPackage rec { pname = "jupyterlab-git"; - version = "0.42.0"; + version = "0.50.0rc0"; + pyproject = true; - disabled = pythonOlder "3.6"; + disabled = pythonOlder "3.8"; src = fetchPypi { pname = "jupyterlab_git"; inherit version; - hash = "sha256-GFnox6KnwKWFqsUWY0QYzMShXlH9KFSY3rRJA4RAiCk="; + hash = "sha256-euo8j7jt6oUJfZMF3VnbuM4uhibv+eijiXPO4UwZCiU="; }; nativeBuildInputs = [ - jupyter-packaging + hatch-jupyter-builder + hatch-nodejs-version + hatchling + jupyterlab ]; propagatedBuildInputs = [ @@ -37,17 +44,20 @@ buildPythonPackage rec { git nbformat pexpect + traitlets ]; nativeCheckInputs = [ jupyterlab pytest-asyncio + pytest-jupyter pytest-tornasync pytestCheckHook ]; - # All Tests on darwin fail or are skipped due to sandbox - doCheck = !stdenv.isDarwin; + preCheck = '' + export HOME=$TMPDIR + ''; disabledTestPaths = [ "jupyterlab_git/tests/test_handlers.py" @@ -67,6 +77,8 @@ buildPythonPackage rec { "jupyterlab_git" ]; + __darwinAllowLocalNetworking = true; + meta = with lib; { description = "Jupyter lab extension for version control with Git"; homepage = "https://github.com/jupyterlab/jupyterlab-git"; diff --git a/pkgs/development/python-modules/mdtraj/default.nix b/pkgs/development/python-modules/mdtraj/default.nix new file mode 100644 index 0000000000000..ad20cdbf06711 --- /dev/null +++ b/pkgs/development/python-modules/mdtraj/default.nix @@ -0,0 +1,102 @@ +{ lib +, stdenv +, buildPythonPackage +, fetchFromGitHub +, fetchpatch +, llvmPackages +, zlib +, cython +, oldest-supported-numpy +, setuptools +, wheel +, astunparse +, numpy +, pyparsing +, scipy +, gsd +, networkx +, pandas +, pytest-xdist +, pytestCheckHook +, tables +}: + +buildPythonPackage rec { + pname = "mdtraj"; + version = "1.9.9"; + pyproject = true; + + src = fetchFromGitHub { + owner = "mdtraj"; + repo = "mdtraj"; + rev = "refs/tags/${version}"; + hash = "sha256-2Jg6DyVJlRBLD/6hMtcsrAdxKF5RkpUuhAQm/lqVGeE="; + }; + + patches = [ + (fetchpatch { + name = "gsd_3-compatibility.patch"; + url = "https://github.com/mdtraj/mdtraj/commit/81209d00817ab07cfc4668bf5ec88088d16904c0.patch"; + hash = "sha256-ttNmij7csxF0Z5wPPwhGumRX055W2IgFjRAe6nI6GNY="; + }) + ]; + + nativeBuildInputs = [ + cython + oldest-supported-numpy + setuptools + wheel + ]; + + buildInputs = [ + zlib + ] ++ lib.optionals stdenv.cc.isClang [ + llvmPackages.openmp + ]; + + propagatedBuildInputs = [ + astunparse + numpy + pyparsing + scipy + ]; + + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-incompatible-function-pointer-types"; + + nativeCheckInputs = [ + gsd + networkx + pandas + pytest-xdist + pytestCheckHook + tables + ]; + + preCheck = '' + cd tests + export PATH=$out/bin:$PATH + ''; + + disabledTests = [ + # require network access + "test_pdb_from_url" + "test_1vii_url_and_gz" + + # fail due to data race + "test_read_atomindices_1" + "test_read_atomindices_2" + + # flaky test + "test_distances_t" + ]; + + pythonImportsCheck = [ "mdtraj" ]; + + meta = with lib; { + description = "An open library for the analysis of molecular dynamics trajectories"; + homepage = "https://github.com/mdtraj/mdtraj"; + changelog = "https://github.com/mdtraj/mdtraj/releases/tag/${src.rev}"; + license = licenses.lgpl21Plus; + maintainers = with maintainers; [ natsukium ]; + }; +} diff --git a/pkgs/development/python-modules/openllm-client/default.nix b/pkgs/development/python-modules/openllm-client/default.nix index 2dd395bab677f..ce77953f12df7 100644 --- a/pkgs/development/python-modules/openllm-client/default.nix +++ b/pkgs/development/python-modules/openllm-client/default.nix @@ -5,11 +5,11 @@ , hatch-fancy-pypi-readme , hatch-vcs , hatchling -, attrs -, cattrs +, anyio +, distro , httpx +, httpx-auth , openllm-core -, orjson , soundfile , transformers }: @@ -30,16 +30,19 @@ buildPythonPackage rec { ]; propagatedBuildInputs = [ - attrs - cattrs + anyio + distro httpx - orjson + openllm-core ]; passthru.optional-dependencies = { grpc = [ bentoml ] ++ bentoml.optional-dependencies.grpc; + auth = [ + httpx-auth + ]; agents = [ transformers # diffusers diff --git a/pkgs/development/python-modules/openllm-core/default.nix b/pkgs/development/python-modules/openllm-core/default.nix index 75b755740d041..ab39bf6c11b91 100644 --- a/pkgs/development/python-modules/openllm-core/default.nix +++ b/pkgs/development/python-modules/openllm-core/default.nix @@ -4,10 +4,12 @@ , pythonOlder , accelerate , attrs -, bentoml , bitsandbytes +, bentoml , cattrs +, click-option-group , datasets +, deepmerge , hatch-fancy-pypi-readme , hatch-vcs , hatchling @@ -15,14 +17,13 @@ , mypy-extensions , orjson , peft -, ray , transformers , typing-extensions }: buildPythonPackage rec { pname = "openllm-core"; - version = "0.3.9"; + version = "0.4.22"; pyproject = true; disabled = pythonOlder "3.8"; @@ -31,7 +32,7 @@ buildPythonPackage rec { owner = "bentoml"; repo = "OpenLLM"; rev = "refs/tags/v${version}"; - hash = "sha256-M/ckvaHTdKFg7xfUgFxu7pRBrS6TGw0m2U3L88b2DKU="; + hash = "sha256-Hgwc4rneY0d7KZHuBIWRpndLksts5DTvaYuwZOO4sdI="; }; sourceRoot = "source/openllm-core"; @@ -44,8 +45,10 @@ buildPythonPackage rec { propagatedBuildInputs = [ attrs - bentoml cattrs + # not listed in pyproject.toml, but required at runtime + click-option-group + deepmerge inflection mypy-extensions orjson @@ -54,9 +57,11 @@ buildPythonPackage rec { passthru.optional-dependencies = { vllm = [ - ray # vllm ]; + bentoml = [ + bentoml + ]; fine-tune = [ accelerate bitsandbytes @@ -67,7 +72,7 @@ buildPythonPackage rec { ] ++ transformers.optional-dependencies.torch ++ transformers.optional-dependencies.tokenizers ++ transformers.optional-dependencies.accelerate; - full = with passthru.optional-dependencies; ( vllm ++ fine-tune ); + full = with passthru.optional-dependencies; ( vllm ++ bentoml ++ fine-tune ); }; # there is no tests diff --git a/pkgs/development/python-modules/openllm/default.nix b/pkgs/development/python-modules/openllm/default.nix index b9f3d2b6fa3b5..b1cad320a11d3 100644 --- a/pkgs/development/python-modules/openllm/default.nix +++ b/pkgs/development/python-modules/openllm/default.nix @@ -9,20 +9,18 @@ , accelerate , bentoml , bitsandbytes +, build , click +, ctranslate2 , datasets , docker , einops -, fairscale -, flax , ghapi +, huggingface-hub , hypothesis , ipython -, jax -, jaxlib , jupyter , jupytext -, keras , nbformat , notebook , openai @@ -34,14 +32,12 @@ , pytest-randomly , pytest-rerunfailures , pytest-xdist -, ray , safetensors , scipy , sentencepiece , soundfile , syrupy , tabulate -, tensorflow , tiktoken , transformers , openai-triton @@ -73,12 +69,16 @@ buildPythonPackage rec { accelerate bentoml bitsandbytes + build click + einops ghapi openllm-client openllm-core optimum safetensors + scipy + sentencepiece tabulate transformers ] ++ bentoml.optional-dependencies.io @@ -92,62 +92,43 @@ buildPythonPackage rec { soundfile transformers ] ++ transformers.optional-dependencies.agents; + awq = [ + # autoawq + ]; baichuan = [ # cpm-kernels - sentencepiece ]; chatglm = [ # cpm-kernels - sentencepiece + ]; + ctranslate = [ + ctranslate2 ]; falcon = [ - einops xformers ]; fine-tune = [ - accelerate - bitsandbytes datasets + huggingface-hub peft # trl ]; - flan-t5 = [ - flax - jax - jaxlib - keras - tensorflow - ]; ggml = [ # ctransformers ]; gptq = [ # auto-gptq - optimum ]; # ++ autogptq.optional-dependencies.triton; grpc = [ - openllm-client - ] ++ openllm-client.optional-dependencies.grpc; - llama = [ - fairscale - sentencepiece - scipy - ]; + bentoml + ] ++ bentoml.optional-dependencies.grpc; mpt = [ - einops openai-triton ]; openai = [ openai tiktoken - ] ++ openai.optional-dependencies.embeddings; - opt = [ - flax - jax - jaxlib - keras - tensorflow - ]; + ] ++ openai.optional-dependencies.datalib; playground = [ ipython jupyter @@ -159,11 +140,10 @@ buildPythonPackage rec { bitsandbytes ]; vllm = [ - ray # vllm ]; full = with passthru.optional-dependencies; ( - agents ++ baichuan ++ chatglm ++ falcon ++ fine-tune ++ flan-t5 ++ ggml ++ gptq ++ llama ++ mpt ++ openai ++ opt ++ playground ++ starcoder ++ vllm + agents ++ awq ++ baichuan ++ chatglm ++ ctranslate ++ falcon ++ fine-tune ++ ggml ++ gptq ++ mpt ++ openai ++ playground ++ starcoder ++ vllm ); all = passthru.optional-dependencies.full; }; @@ -187,12 +167,15 @@ buildPythonPackage rec { export CI=1 ''; + disabledTestPaths = [ + # require network access + "tests/models" + ]; + disabledTests = [ - # these tests access to huggingface.co - "test_opt_125m" - "test_opt_125m" - "test_flan_t5" - "test_flan_t5" + # incompatible with recent TypedDict + # https://github.com/bentoml/OpenLLM/blob/f3fd32d596253ae34c68e2e9655f19f40e05f666/openllm-python/tests/configuration_test.py#L18-L21 + "test_missing_default" ]; pythonImportsCheck = [ "openllm" ]; diff --git a/pkgs/development/python-modules/xkcdpass/default.nix b/pkgs/development/python-modules/xkcdpass/default.nix index 5b253d3260a89..d4a04317ad800 100644 --- a/pkgs/development/python-modules/xkcdpass/default.nix +++ b/pkgs/development/python-modules/xkcdpass/default.nix @@ -1,7 +1,6 @@ { lib , buildPythonPackage , fetchPypi -, fetchpatch , installShellFiles , pytestCheckHook , pythonAtLeast @@ -10,24 +9,16 @@ buildPythonPackage rec { pname = "xkcdpass"; - version = "1.19.5"; + version = "1.19.6"; format = "setuptools"; disabled = pythonOlder "3.7"; src = fetchPypi { inherit pname version; - hash = "sha256-zEgC3tTQ6kwDovHPHRTvYndWVF79DpnAX454VDZiedE="; + hash = "sha256-zrdR4KuORCGIoRTZDednT9JDV/seWQRa3aPal8gxdTE="; }; - patches = [ - (fetchpatch { - name = "fix-non-deterministic-test.patch"; - url = "https://github.com/redacted/XKCD-password-generator/commit/72d174a82822af1934c94de1b66fd956230142f5.patch"; - hash = "sha256-GES40GHM0+Zx8bRceCy9/fOHJVlWZ7TCLfzhZczjfTE="; - }) - ]; - nativeBuildInputs = [ installShellFiles ]; |