From a575ec4c6f094edc4ae83ba48ac38eddf24bfe57 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Mon, 2 Oct 2023 01:11:23 -0500 Subject: [PATCH 1/9] fix: fix m1 sopht installation issue with modifed pyfftw and pystencils from git. Version control on some dependcies are modified --- poetry.lock | 839 ++++++++++++++++++++++++++----------------------- pyproject.toml | 8 +- 2 files changed, 448 insertions(+), 399 deletions(-) diff --git a/poetry.lock b/poetry.lock index 60cc67f..f397e7b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -47,24 +47,24 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "cfgv" -version = "3.3.1" +version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" files = [ - {file = "cfgv-3.3.1-py2.py3-none-any.whl", hash = "sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426"}, - {file = "cfgv-3.3.1.tar.gz", hash = "sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736"}, + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, + {file = "cfgv-3.4.0.tar.gz", hash = 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"magneto_pyelastica"] @@ -1324,4 +1373,4 @@ examples = ["click", "coomm", "magneto_pyelastica"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.11" -content-hash = "fdec2e95ced45153b284873aeb1efff60167658d993379e08754be5b80ea4d18" +content-hash = "95904f559b5e09b0b5a57c744448a6de5157db9c3ac00016bf4ec747fba489dd" diff --git a/pyproject.toml b/pyproject.toml index 4038d9d..4a11502 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,15 +20,15 @@ packages = [ [tool.poetry.dependencies] python = ">=3.10,<3.11" numpy = "^1.20.0" -numba = "^0.55" -pystencils = "^1.0" +numba = ">=0.55" scipy = "^1.7.3" sympy = "^1.9" -pyfftw = "^0.13.0" psutil = "^5.9.0" h5py = "^3.6" pyelastica = "^0.3" -matplotlib = "^3.3.2" +matplotlib = "3.7.1" +pyfftw = { git="https://github.com/tp5uiuc/pyFFTW.git", branch="macos_fix" } +pystencils = { git="https://github.com/sy-cui/pystencils.git", branch="macos_fix" } click = {version = "^8.1", optional = true, extras = ["examples"]} coomm = {version = ">=0.1.1", optional = true, extras = ["examples"]} magneto_pyelastica = {version = ">=0.0.1", optional = true, extras = ["examples"]} From e5ed18df704b343a3b46888a520c0c7708aa5d95 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Mon, 2 Oct 2023 01:12:22 -0500 Subject: [PATCH 2/9] feat: environment.yml file for environment initialization --- environment.yml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..f420c46 --- /dev/null +++ b/environment.yml @@ -0,0 +1,7 @@ +name: sopht-env +channels: + - defaults +dependencies: + - python=3.10.* + - pip + - conda-forge::poetry>=1.0.0,<1.6.0 From 210f4a517adca527699a242524b1e27045c308e7 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Mon, 2 Oct 2023 01:23:39 -0500 Subject: [PATCH 3/9] update README.md --- README.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 81e8715..359ef6b 100644 --- a/README.md +++ b/README.md @@ -19,20 +19,19 @@ the project, although most of the important commands will be provided in `Makefi First **create the fork repository and clone** to your local machine. -2. Virtual python workspace: `conda`, `pyenv`, or `venv`. +2. Virtual python workspace: `conda`. -We recommend using python version above 3.10. +A `environment.yml` file is provided to easily create a virtual environment +named `sopht-env`. The user may modify the name as necessary. ```bash -conda create --name sopht-env +conda env create -f environment.yml conda activate sopht-env -conda install pip ``` -3. Setup [`poetry`](https://python-poetry.org) and `dependencies`! +3. Set up `dependencies`! ```bash -make poetry-download make install make pre-commit-install ``` @@ -48,7 +47,7 @@ We ask that any publications which use SophT cite as following: Songyuan Cui and Fan Kiat Chan and Mattia Gazzola}, - title = {{Scalable One-stop Platform for Hydroelastic Things + title = {{Scalable One-stop Platform for Hydroelastic Things (SOPHT)}}, month = feb, year = 2023, @@ -64,4 +63,3 @@ We ask that any publications which use SophT cite as following: [link-doi]: https://zenodo.org/badge/latestdoi/498451510 [link-CI]: https://github.com/SophT-Team/SophT/actions - From 164765a054aa686b6c52e737618962559ea14a8e Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Mon, 2 Oct 2023 19:49:59 -0500 Subject: [PATCH 4/9] fix: update poetry.lock to reflect changes in pystencils --- poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index f397e7b..6319591 100644 --- a/poetry.lock +++ b/poetry.lock @@ -929,13 +929,13 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa [[package]] name = "platformdirs" -version = "3.10.0" +version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." optional = false python-versions = ">=3.7" files = [ - {file = "platformdirs-3.10.0-py3-none-any.whl", hash = "sha256:d7c24979f292f916dc9cbf8648319032f551ea8c49a4c9bf2fb556a02070ec1d"}, - {file = "platformdirs-3.10.0.tar.gz", hash = "sha256:b45696dab2d7cc691a3226759c0d3b00c47c8b6e293d96f6436f733303f77f6d"}, + {file = "platformdirs-3.11.0-py3-none-any.whl", hash = "sha256:e9d171d00af68be50e9202731309c4e658fd8bc76f55c11c7dd760d023bda68e"}, + {file = "platformdirs-3.11.0.tar.gz", hash = "sha256:cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3"}, ] [package.extras] @@ -1107,7 +1107,7 @@ use-cython = ["Cython"] type = "git" url = "https://github.com/sy-cui/pystencils.git" reference = "macos_fix" -resolved_reference = "8b8e92bb296f0ea64702c1c84195f9981ab0e023" +resolved_reference = "b79d384e694f39c65fcd98ea6ea0c61d968895f4" [[package]] name = "pytest" From 98e9b4cf4d26c172e23469f95448b62391990817 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Tue, 3 Oct 2023 11:27:08 -0500 Subject: [PATCH 5/9] refactor: make pystencils and pyfftw installation os-dependent --- poetry.lock | 68 +++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 11 ++++++-- 2 files changed, 76 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6319591..9e672bb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1033,6 +1033,48 @@ tqdm = ">=4.61.1,<5.0.0" docs = ["Sphinx (>=6.1,<7.0)", "docutils (>=0.18,<0.19)", "myst-parser (>=1.0,<2.0)", "numpydoc (>=1.3.1,<2.0.0)", "readthedocs-sphinx-search (>=0.1.1,<0.2.0)", "sphinx-autodoc-typehints (>=1.21,<2.0)", "sphinx-book-theme (>=1.0,<2.0)"] examples = ["cma (>=3.2.2,<4.0.0)", "matplotlib (>=3.3.2,<4.0.0)"] +[[package]] +name = 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["islpy", "py-cpuinfo"] +bench-db = ["blitzdb", "pandas", "pymongo"] +doc = ["nbsphinx", "pandoc", "sphinx", "sphinx_autodoc_typehints", "sphinx_rtd_theme", "sphinxcontrib-bibtex"] +gpu = ["cupy"] +interactive = ["graphviz", "imageio", "ipy_table", "jupyter", "matplotlib", "pyevtk", "rich"] +use-cython = ["Cython"] + [[package]] name = "pytest" version = "7.4.2" @@ -1373,4 +1439,4 @@ examples = ["click", "coomm", "magneto_pyelastica"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.11" -content-hash = "95904f559b5e09b0b5a57c744448a6de5157db9c3ac00016bf4ec747fba489dd" +content-hash = "5fde9d1c44a26a629be16c51c671363b0c21ae00eeec19fd9a3869907202c90e" diff --git a/pyproject.toml b/pyproject.toml index 4a11502..e746866 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,8 +27,15 @@ psutil = "^5.9.0" h5py = "^3.6" pyelastica = "^0.3" matplotlib = "3.7.1" -pyfftw = { git="https://github.com/tp5uiuc/pyFFTW.git", branch="macos_fix" } -pystencils = { git="https://github.com/sy-cui/pystencils.git", branch="macos_fix" } +pyfftw = [ + { version="^0.13.0", markers="sys_platform != 'darwin'", source="pypi"}, + { git="https://github.com/tp5uiuc/pyFFTW.git", branch="macos_fix", markers="sys_platform == 'darwin'" }, +] +pystencils = [ + { version="^1.0", markers="sys_platform != 'darwin'", source="pypi"}, + { git="https://github.com/sy-cui/pystencils.git", branch="macos_fix", markers="sys_platform == 'darwin'" }, + +] click = {version = "^8.1", optional = true, extras = ["examples"]} coomm = {version = ">=0.1.1", optional = true, extras = ["examples"]} magneto_pyelastica = {version = ">=0.0.1", optional = true, extras = ["examples"]} From ecca1370e7180fb611f794f67407b30854baf1c3 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Tue, 10 Oct 2023 23:27:06 -0500 Subject: [PATCH 6/9] fix: remove conda-forge channel requirement from poetry installation --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index f420c46..baadc86 100644 --- a/environment.yml +++ b/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - python=3.10.* - pip - - conda-forge::poetry>=1.0.0,<1.6.0 + - poetry>=1.0.0,<1.6.0 From 457cbfd8bcc8cbc472f5455505130c360fd061d0 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Wed, 11 Oct 2023 13:28:17 -0500 Subject: [PATCH 7/9] refactor: remove environment.yml and install poetry using pip --- Makefile | 8 ++++---- environment.yml | 7 ------- 2 files changed, 4 insertions(+), 11 deletions(-) delete mode 100644 environment.yml diff --git a/Makefile b/Makefile index 00dde30..dc75af2 100644 --- a/Makefile +++ b/Makefile @@ -2,13 +2,13 @@ PYTHON := python3 PYTHONPATH := `pwd` #* Poetry -.PHONY: poetry-download -poetry-download: - curl -sSL https://install.python-poetry.org/ | $(PYTHON) - +.PHONY: poetry-install +poetry-install: + pip install "poetry>=1.0.0,<1.6.0" .PHONY: poetry-remove poetry-remove: - curl -sSL https://install.python-poetry.org/ | $(PYTHON) - --uninstall + pip uninstall poetry #* Installation .PHONY: install diff --git a/environment.yml b/environment.yml deleted file mode 100644 index baadc86..0000000 --- a/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: sopht-env -channels: - - defaults -dependencies: - - python=3.10.* - - pip - - poetry>=1.0.0,<1.6.0 From 44e96cfe06b568ee62762d3392dd954357177762 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Wed, 11 Oct 2023 13:33:58 -0500 Subject: [PATCH 8/9] doc: udpate installation instruction in README.md --- README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 359ef6b..9d37871 100644 --- a/README.md +++ b/README.md @@ -19,19 +19,18 @@ the project, although most of the important commands will be provided in `Makefi First **create the fork repository and clone** to your local machine. -2. Virtual python workspace: `conda`. - -A `environment.yml` file is provided to easily create a virtual environment -named `sopht-env`. The user may modify the name as necessary. +2. Set up virtual python workspace: `conda`. ```bash -conda env create -f environment.yml +conda create -n sopht-env conda activate sopht-env +conda install python=3.10 ``` 3. Set up `dependencies`! ```bash +make poetry-install make install make pre-commit-install ``` From f7d8b6244cc18ef4bbe95399fbb832e65ce4f505 Mon Sep 17 00:00:00 2001 From: Songyuan Cui Date: Mon, 16 Oct 2023 12:09:09 -0500 Subject: [PATCH 9/9] doc: update README.md with instructions for MacOS installation --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9d37871..6eb40ff 100644 --- a/README.md +++ b/README.md @@ -26,8 +26,17 @@ conda create -n sopht-env conda activate sopht-env conda install python=3.10 ``` +3. (MacOS) System-wide installed dependencies -3. Set up `dependencies`! +On MacOS (especially M-series with ARM64 architecture), we require a Homebrew installed +`fftw` library and a working `clang++` compiler with `OpenMP` support. If these requirements +are not met, we recommend +```bash +brew install llvm +brew install fftw +``` + +4. Set up `dependencies`! ```bash make poetry-install