From 682cfe78a642eccc249ef1477b3748f1a850bf0c Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 16:27:56 -0700 Subject: [PATCH 01/10] feat: Add pixi project configuration * Add pixi support for linux-64, osx-64, and osx-arm64 machines. * Update README and notebooks to add pixi instructions. * Fix typo in Makefile. --- .gitattributes | 2 + .gitignore | 4 + Makefile | 2 +- README.md | 18 + pixi.lock | 5938 ++++++++++++++++++++++++++++++++++++++++++++++++ pixi.toml | 33 + 6 files changed, 5996 insertions(+), 1 deletion(-) create mode 100644 .gitattributes create mode 100644 pixi.lock create mode 100644 pixi.toml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..8f61a8e --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting +pixi.lock linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index ff6f4b0..8df395d 100644 --- a/.gitignore +++ b/.gitignore @@ -136,3 +136,7 @@ book/1Lbb-likelihoods/ # Mac artifacts .DS_Store + +# pixi environments +.pixi +*.egg-info diff --git a/Makefile b/Makefile index e3eda41..4d6bf2a 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ all: build -defualt: build +default: build build: jupyter-book build book/ diff --git a/README.md b/README.md index 6d7dd8f..89ce6e1 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,16 @@ ## Setup +### Using `pixi` (recommended) + +On any `x86` Linux machine or any macOS machine first install [`pixi`](https://pixi.sh/) and then from the top level of the repository run + +``` +pixi run start +``` + +### Using a manually controlled virtual environment + In a Python virtual environment run the following ``` @@ -21,6 +31,14 @@ python -m pip install --require-hashes --requirement book/requirements.lock To build the book after setup simply run +### Using `pixi` + +``` +pixi run build +``` + +### Local virtual environment + ``` make build ``` diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..b4cc1e2 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,5938 @@ +version: 6 +environments: + default: + channels: + - 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__osx >=11.0 + - libzlib >=1.2.13,<2.0.0a0 + arch: arm64 + platform: osx + license: BSD-3-Clause + license_family: BSD + size: 405089 + timestamp: 1714723101397 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 0000000..54ead3d --- /dev/null +++ b/pixi.toml @@ -0,0 +1,33 @@ +[project] +authors = ["Matthew Feickert "] +channels = ["conda-forge"] +description = "pyhf user guide" +name = "pyhf-tutorial" +platforms = ["linux-64", "osx-64", "osx-arm64"] +version = "0.1.0" + +[tasks.build] +description = "Build the Jupyter Book" +cmd = "jupyter-book build book/" + +[tasks.start] +description = "Launch Jupyer Lab and explore the user guide notebooks" +cmd = "jupyter lab" + +[dependencies] +python = "3.12.*" +pyhf = "0.7.5.*" +uproot = ">=5.5.1,<6" +iminuit = ">=2.30.1,<3" +matplotlib-base = ">=3.10.0,<4" +requests = ">=2.32.3,<3" +# visualization +ipywidgets = ">=8.1.5,<9" +ipympl = ">=0.9.5,<0.10" +pandas = ">=2.2.3,<3" +altair = ">=5.5.0,<6" +rich = ">=13.9.4,<14" +# jupyter notebooks +notebook = ">=7.3.2,<8" +jupyterlab = ">=4.3.4,<5" +jupyter-book = "0.15.1.*" From 05659d3ac0a27bf08b826432e0cf33f3afa70bd3 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 16:41:13 -0700 Subject: [PATCH 02/10] Add pixi instructions to book --- book/introduction.md | 38 +++++++++++++++++++++++++++++++++----- 1 file changed, 33 insertions(+), 5 deletions(-) diff --git a/book/introduction.md b/book/introduction.md index b3d14ea..00055ce 100644 --- a/book/introduction.md +++ b/book/introduction.md @@ -25,11 +25,17 @@ Instead, let's move to looking at the `pyhf` API right away. ::::{tab-set} -:::{tab-item} Locally +:::{tab-item} With pixi +``` +$ pixi init +$ pixi shell +``` + +:::{tab-item} With venv ``` $ python3 -m venv pyhf-tutorial $ source pyhf-tutorial/bin/activate -(pyhf-tutorial) $ python -m pip install --upgrade pip setuptools wheel +(pyhf-tutorial) $ python -m pip install --upgrade pip ``` ::: @@ -48,7 +54,7 @@ Then we can go ahead and create the virtual environment ``` $ python3 -m venv pyhf-tutorial $ source pyhf-tutorial/bin/activate -(pyhf-tutorial) $ python -m pip install --upgrade pip setuptools wheel +(pyhf-tutorial) $ python -m pip install --upgrade pip ``` ::: @@ -67,7 +73,7 @@ Then we can go ahead and create the virtual environment ``` $ python3 -m venv pyhf-tutorial $ source pyhf-tutorial/bin/activate -(pyhf-tutorial) $ python -m pip install --upgrade pip setuptools wheel +(pyhf-tutorial) $ python -m pip install --upgrade pip ``` ::: @@ -92,7 +98,13 @@ If you haven't already, make a new Python 3 virtual environment and then install (pyhf-tutorial) $ python -m pip install pyhf ``` - or [Conda-forge](https://anaconda.org/conda-forge/pyhf) +or from [conda-forge](https://anaconda.org/conda-forge/pyhf) using [`pixi`](https://pixi.sh/) + +``` +$ pixi add pyhf +``` + +or [`conda`](https://docs.conda.io/) ``` (pyhf-tutorial) $ conda install --channel conda-forge pyhf @@ -141,6 +153,22 @@ To get all the dependencies needed for this tutorial first clone the repository (pyhf-tutorial) $ cd pyhf-tutorial ``` +#### Using pixi + +Simply run + +``` +pixi install +``` + +or to also start running the example notebooks run + +``` +pixi run start +``` + +#### Using pip + then you can just install from the included `requirements.txt` in the top level `binder/` directory of [the source repository](https://github.com/pyhf/pyhf-tutorial) ``` From 96bf0894b3b4d46469d29fdd6cbd101fb5b0d39a Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 16:45:45 -0700 Subject: [PATCH 03/10] Add clean task --- pixi.toml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pixi.toml b/pixi.toml index 54ead3d..5518266 100644 --- a/pixi.toml +++ b/pixi.toml @@ -10,6 +10,10 @@ version = "0.1.0" description = "Build the Jupyter Book" cmd = "jupyter-book build book/" +[tasks.clean] +description = "Remove the Jupyter Book build" +cmd = "rm -rf book/_build" + [tasks.start] description = "Launch Jupyer Lab and explore the user guide notebooks" cmd = "jupyter lab" From 5086289662445c7ee936e33fcea16efabceeccf4 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 16:50:55 -0700 Subject: [PATCH 04/10] fixup formatting --- book/introduction.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/book/introduction.md b/book/introduction.md index 00055ce..669fcb2 100644 --- a/book/introduction.md +++ b/book/introduction.md @@ -30,6 +30,7 @@ Instead, let's move to looking at the `pyhf` API right away. $ pixi init $ pixi shell ``` +::: :::{tab-item} With venv ``` @@ -153,7 +154,7 @@ To get all the dependencies needed for this tutorial first clone the repository (pyhf-tutorial) $ cd pyhf-tutorial ``` -#### Using pixi +#### Using `pixi` Simply run @@ -167,9 +168,9 @@ or to also start running the example notebooks run pixi run start ``` -#### Using pip +#### Using `pip` -then you can just install from the included `requirements.txt` in the top level `binder/` directory of [the source repository](https://github.com/pyhf/pyhf-tutorial) +Install from the included `requirements.txt` in the top level `binder/` directory of [the source repository](https://github.com/pyhf/pyhf-tutorial) ``` (pyhf-tutorial) $ python -m pip install --upgrade --requirement binder/requirements.txt From 8d967d3bbb2093a5eba8b91cc0608d913d265154 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 17:07:19 -0700 Subject: [PATCH 05/10] Add pixi and conda install directions --- book/introduction.md | 35 +++++++++++++++++++++++++++-------- 1 file changed, 27 insertions(+), 8 deletions(-) diff --git a/book/introduction.md b/book/introduction.md index 669fcb2..5492d72 100644 --- a/book/introduction.md +++ b/book/introduction.md @@ -40,6 +40,13 @@ $ source pyhf-tutorial/bin/activate ``` ::: +:::{tab-item} With conda +``` +$ conda create --name pyhf-tutorial --yes 'python=3.12' +$ conda activate pyhf-tutorial +``` +::: + :::{tab-item} On CC7 lxplus/tier-3 First we need to set up the 'views' with the right paths to ensure we use the correct `pip` @@ -89,27 +96,39 @@ Not all parts of this user guide are able to run in Pyodide, but the pure Python :::: -Once you have a virtual environment set up, you can use `source pyhf-tutorial/bin/activate` to get back into it again. Note the prefix `(pyhf-tutorial) $` on your command line, which indicates that you're inside a virtual environment named 'pyhf-tutorial'. +Once you have a virtual environment set up, you can use `source pyhf-tutorial/bin/activate` to get back into it again (or `pixi shell` for `pixi`). Note the prefix `(pyhf-tutorial) $` on your command line, which indicates that you're inside a virtual environment named 'pyhf-tutorial'. ### Getting pyhf -If you haven't already, make a new Python 3 virtual environment and then install `pyhf` from either [PyPI](https://pypi.org/project/pyhf/) with `pip` +If you haven't already, make a new Python 3 virtual environment and then install `pyhf` + +::::{tab-set} + +:::{tab-item} pixi +from [conda-forge](https://anaconda.org/conda-forge/pyhf) with [`pixi`](https://pixi.sh/) ``` -(pyhf-tutorial) $ python -m pip install pyhf +$ pixi add pyhf ``` +::: -or from [conda-forge](https://anaconda.org/conda-forge/pyhf) using [`pixi`](https://pixi.sh/) +:::{tab-item} pip +from [PyPI](https://pypi.org/project/pyhf/) with `pip` ``` -$ pixi add pyhf +(pyhf-tutorial) $ python -m pip install pyhf ``` +::: -or [`conda`](https://docs.conda.io/) +:::{tab-item} conda +from [conda-forge](https://anaconda.org/conda-forge/pyhf) with [`conda`](https://docs.conda.io/) ``` (pyhf-tutorial) $ conda install --channel conda-forge pyhf ``` +::: + +:::: ### Installation Extras @@ -156,7 +175,7 @@ To get all the dependencies needed for this tutorial first clone the repository #### Using `pixi` -Simply run +then simply run ``` pixi install @@ -170,7 +189,7 @@ pixi run start #### Using `pip` -Install from the included `requirements.txt` in the top level `binder/` directory of [the source repository](https://github.com/pyhf/pyhf-tutorial) +then install from the included `requirements.txt` in the top level `binder/` directory of [the source repository](https://github.com/pyhf/pyhf-tutorial) ``` (pyhf-tutorial) $ python -m pip install --upgrade --requirement binder/requirements.txt From b05f543af56982242e480e36054c114784f426c5 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 17:26:24 -0700 Subject: [PATCH 06/10] Update to EL9 --- book/introduction.md | 37 +++++++++++++------------------------ 1 file changed, 13 insertions(+), 24 deletions(-) diff --git a/book/introduction.md b/book/introduction.md index 5492d72..1cb4d12 100644 --- a/book/introduction.md +++ b/book/introduction.md @@ -47,41 +47,30 @@ $ conda activate pyhf-tutorial ``` ::: -:::{tab-item} On CC7 lxplus/tier-3 -First we need to set up the 'views' with the right paths to ensure we use the correct `pip` +:::{tab-item} On EL9 LXPLUS/tier-3 +First we need to set up the 'views' that [already have `pyhf` installed](https://lcginfo.cern.ch/pkg/pyhf/) ``` $ export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase -$ source $ATLAS_LOCAL_ROOT_BASE/user/atlasLocalSetup.sh -$ lsetup "views LCG_98python3 x86_64-centos7-gcc8-opt" -$ export PYTHONPATH=/cvmfs/sft.cern.ch/lcg/views/LCG_98python3/x86_64-centos7-gcc8-opt/python:/cvmfs/sft.cern.ch/lcg/views/LCG_98python3/x86_64-centos7-gcc8-opt/lib +$ . $ATLAS_LOCAL_ROOT_BASE/user/atlasLocalSetup.sh +$ lsetup "views LCG_106 x86_64-el9-gcc13-opt" ``` -Then we can go ahead and create the virtual environment +Then we can install [`cvmfs-venv`](https://github.com/matthewfeickert/cvmfs-venv) ``` -$ python3 -m venv pyhf-tutorial -$ source pyhf-tutorial/bin/activate -(pyhf-tutorial) $ python -m pip install --upgrade pip -``` -::: - -:::{tab-item} On SLC6 lxplus/tier-3 -First we need to set up the 'views' with the right paths to ensure we use the correct `pip` - -``` -$ export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase -$ source $ATLAS_LOCAL_ROOT_BASE/user/atlasLocalSetup.sh -$ lsetup "views LCG_98python3 x86_64-slc6-gcc8-opt" -$ export PYTHONPATH=/cvmfs/sft.cern.ch/lcg/views/LCG_98python3/x86_64-slc6-gcc8-opt/python:/cvmfs/sft.cern.ch/lcg/views/LCG_98python3/x86_64-slc6-gcc8-opt/lib +$ mkdir -p ~/.local/bin +$ export PATH=~/.local/bin:"${PATH}" +$ curl -sL https://raw.githubusercontent.com/matthewfeickert/cvmfs-venv/main/cvmfs-venv.sh -o ~/.local/bin/cvmfs-venv +$ chmod +x ~/.local/bin/cvmfs-venv ``` -Then we can go ahead and create the virtual environment +and use it to create a user controlled virtual environment ``` -$ python3 -m venv pyhf-tutorial -$ source pyhf-tutorial/bin/activate -(pyhf-tutorial) $ python -m pip install --upgrade pip +$ cvmfs-venv pyhf-tutorial +$ . pyhf-tutorial/bin/activate +(pyhf-tutorial) $ uv pip install --upgrade pip ``` ::: From fcb3ca95bd2b47489fd8909d8ca3dfed8c0fb252 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 17:32:52 -0700 Subject: [PATCH 07/10] Update version number --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index 5518266..42b9f70 100644 --- a/pixi.toml +++ b/pixi.toml @@ -4,7 +4,7 @@ channels = ["conda-forge"] description = "pyhf user guide" name = "pyhf-tutorial" platforms = ["linux-64", "osx-64", "osx-arm64"] -version = "0.1.0" +version = "0.7.5" [tasks.build] description = "Build the Jupyter Book" From ffde3361508dc522d4d19242f2c4ef8d7efb36ba Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 17:43:05 -0700 Subject: [PATCH 08/10] Add seperate book environemnt --- README.md | 2 +- pixi.lock | 870 ++++++++++++++++++++++++++++++++++++++++++++++-------- pixi.toml | 21 +- 3 files changed, 764 insertions(+), 129 deletions(-) diff --git a/README.md b/README.md index 89ce6e1..0f57982 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ On any `x86` Linux machine or any macOS machine first install [`pixi`](https://pixi.sh/) and then from the top level of the repository run ``` -pixi run start +pixi install --environment book ``` ### Using a manually controlled virtual environment diff --git a/pixi.lock b/pixi.lock index b4cc1e2..55770a6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,5 +1,726 @@ version: 6 environments: + book: + channels: + - 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-[tasks.clean] -description = "Remove the Jupyter Book build" -cmd = "rm -rf book/_build" - [tasks.start] description = "Launch Jupyer Lab and explore the user guide notebooks" cmd = "jupyter lab" @@ -34,4 +26,17 @@ rich = ">=13.9.4,<14" # jupyter notebooks notebook = ">=7.3.2,<8" jupyterlab = ">=4.3.4,<5" + +[feature.book.dependencies] jupyter-book = "0.15.1.*" + +[feature.book.tasks.build] +description = "Build the Jupyter Book" +cmd = "jupyter-book build book/" + +[feature.book.tasks.clean] +description = "Remove the Jupyter Book build" +cmd = "rm -rf book/_build" + +[environments] +book = ["book"] From a6ac8472c9a77b104e65c49c243dec89320b4f58 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 17:55:10 -0700 Subject: [PATCH 09/10] Add root_base only to Linux --- pixi.lock | 1498 +++++++++++++++++++++++++++++++++++++++++++++++++++++ pixi.toml | 4 + 2 files changed, 1502 insertions(+) diff --git a/pixi.lock b/pixi.lock index 55770a6..a175902 100644 --- a/pixi.lock +++ b/pixi.lock @@ -17,21 +17,27 @@ environments: - 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__glibc >=2.17,<3.0.a0 + - libgcc >=13 + - libzlib 1.3.1 hb9d3cd8_2 + arch: x86_64 + platform: linux + license: Zlib + license_family: Other + size: 92286 + timestamp: 1727963153079 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py312hef9b889_1.conda sha256: b97015e146437283f2213ff0e95abdc8e2480150634d81fbae6b96ee09f5e50b md5: 8b7069e9792ee4e5b4919a7a306d2e67 diff --git a/pixi.toml b/pixi.toml index b3519c7..2b7c57e 100644 --- a/pixi.toml +++ b/pixi.toml @@ -30,6 +30,10 @@ jupyterlab = ">=4.3.4,<5" [feature.book.dependencies] jupyter-book = "0.15.1.*" +# macOS support for ROOT is currently not good +[feature.book.target.linux-64.dependencies] +root_base = ">=6.32.2,<7" + [feature.book.tasks.build] description = "Build the Jupyter Book" cmd = "jupyter-book build book/" From fada968ae9ce28b7501d83d63c84d06e1d3550d5 Mon Sep 17 00:00:00 2001 From: Matthew Feickert Date: Mon, 6 Jan 2025 18:00:16 -0700 Subject: [PATCH 10/10] reposition --- pixi.toml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pixi.toml b/pixi.toml index 2b7c57e..46d96c8 100644 --- a/pixi.toml +++ b/pixi.toml @@ -27,13 +27,6 @@ rich = ">=13.9.4,<14" notebook = ">=7.3.2,<8" jupyterlab = ">=4.3.4,<5" -[feature.book.dependencies] -jupyter-book = "0.15.1.*" - -# macOS support for ROOT is currently not good -[feature.book.target.linux-64.dependencies] -root_base = ">=6.32.2,<7" - [feature.book.tasks.build] description = "Build the Jupyter Book" cmd = "jupyter-book build book/" @@ -42,5 +35,12 @@ cmd = "jupyter-book build book/" description = "Remove the Jupyter Book build" cmd = "rm -rf book/_build" +[feature.book.dependencies] +jupyter-book = "0.15.1.*" + +# macOS support for ROOT is currently not good +[feature.book.target.linux-64.dependencies] +root_base = ">=6.32.2,<7" + [environments] book = ["book"]