From 142ff493e48327ce6d0b2c51b59eccec1b542f80 Mon Sep 17 00:00:00 2001
From: Guillaume Lemaitre <guillaume@probabl.ai>
Date: Sat, 18 May 2024 20:08:49 +0200
Subject: [PATCH] MAINT create a dev environment containing all dependencies
 (#85)

---
 .github/workflows/deploy-gh-pages.yml |    2 +-
 .github/workflows/lint.yml            |    2 +-
 doc/quick_start.rst                   |   17 +
 pixi.lock                             | 3199 ++++++++++++++++++++++++-
 pyproject.toml                        |    2 +
 5 files changed, 3146 insertions(+), 76 deletions(-)

diff --git a/.github/workflows/deploy-gh-pages.yml b/.github/workflows/deploy-gh-pages.yml
index 7a75db0..5c3f543 100644
--- a/.github/workflows/deploy-gh-pages.yml
+++ b/.github/workflows/deploy-gh-pages.yml
@@ -23,7 +23,7 @@ jobs:
         frozen: true
 
     - name: Build documentation
-      run: pixi run build-doc
+      run: pixi run -e doc build-doc
 
     - name: Update the main gh-page website
       if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index f61e034..cf81313 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -20,4 +20,4 @@ jobs:
           frozen: true
 
       - name: Run linter
-        run: pixi run lint
+        run: pixi run -e lint lint
diff --git a/doc/quick_start.rst b/doc/quick_start.rst
index 0807e40..1a1636f 100644
--- a/doc/quick_start.rst
+++ b/doc/quick_start.rst
@@ -134,6 +134,23 @@ In addition, you have a linter task to check the code consistency in terms of st
 
   pixi run lint
 
+Activating the development environment
+--------------------------------------
+
+In the case that you don't want to use the `pixi run` commands and directly interact
+with the usual python tools, you can activate the development environment:
+
+.. prompt:: bash $
+
+  pixi shell -e dev
+
+This will activate an environment containing the dependencies needed to run the linters,
+tests, and build the documentation. So for instance, you can run the tests with:
+
+.. prompt:: bash $
+
+  pytest -vsl skltemplate
+
 Setup the continuous integration
 --------------------------------
 
diff --git a/pixi.lock b/pixi.lock
index 8916d4a..4cd9068 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -137,6 +137,632 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/win-64/vs2015_runtime-14.38.33130-hcb4865c_18.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/xz-5.2.6-h8d14728_0.tar.bz2
       - pypi: .
+  dev:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/accessible-pygments-0.0.4-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.14.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.12.3-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/black-23.3.0-py311h38be061_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py311hb755f60_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.1-py311h9547e67_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/coverage-7.5.1-py311h331c9d8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.8-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.14.0-pyhd8ed1ab_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.51.0-py311h459d7ec_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/glib-2.80.2-hf974151_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.24.3-h9ad1361_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.24.3-haf2f30d_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda
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   size: 18980
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-  - gettext >=0.21.1,<1.0a0
-  - gstreamer 1.24.1 h98fc4e7_1
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   - libexpat >=2.6.2,<3.0a0
   - libgcc-ng >=12
   - libglib >=2.80.0,<3.0a0
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   - libzlib >=1.2.13,<1.3.0a0
-  - xorg-libx11 >=1.8.7,<2.0a0
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   - xorg-libxau >=1.0.11,<2.0a0
   - xorg-libxext >=1.3.4,<2.0a0
   - xorg-libxrender >=0.9.11,<0.10.0a0
   license: LGPL-2.0-or-later
   license_family: LGPL
-  size: 2789211
-  timestamp: 1711318581613
+  size: 2794610
+  timestamp: 1714842288833
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+  name: gst-plugins-base
+  version: 1.24.3
+  build: hba88be7_0
+  subdir: win-64
+  url: https://conda.anaconda.org/conda-forge/win-64/gst-plugins-base-1.24.3-hba88be7_0.conda
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+  license_family: LGPL
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+  timestamp: 1714842910504
 - kind: conda
   name: gstreamer
   version: 1.24.1
@@ -2436,6 +3689,45 @@ packages:
   license_family: LGPL
   size: 2069365
   timestamp: 1711318923388
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+  license: LGPL-2.0-or-later
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+  url: https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.24.3-haf2f30d_0.conda
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+  license_family: LGPL
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 - kind: conda
   name: harfbuzz
   version: 8.4.0
@@ -2456,6 +3748,26 @@ packages:
   license_family: MIT
   size: 1587652
   timestamp: 1713957638950
+- kind: conda
+  name: harfbuzz
+  version: 8.5.0
+  build: hfac3d4d_0
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+  url: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.5.0-hfac3d4d_0.conda
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+  - libstdcxx-ng >=12
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+  license_family: MIT
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 - kind: conda
   name: icu
   version: '73.2'
@@ -2487,6 +3799,24 @@ packages:
   license_family: MIT
   size: 13422193
   timestamp: 1692901469029
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+  build: pyhd8ed1ab_0
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+  md5: ba68cb5105760379432cebc82b45af40
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   name: idna
   version: '3.7'
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   size: 111589
   timestamp: 1704967140287
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+  build: pyhd8ed1ab_0
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   name: joblib
   version: 1.4.0
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   size: 220154
   timestamp: 1712597317378
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+  build: pyhd8ed1ab_0
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   version: 1.6.1
@@ -2618,6 +3984,86 @@ packages:
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   size: 117831
   timestamp: 1646151697040
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+  url: https://conda.anaconda.org/conda-forge/osx-64/kiwisolver-1.4.5-py311h5fe6e05_1.conda
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   size: 25328763
   timestamp: 1714517601407
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+  license_family: Apache
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+  url: https://conda.anaconda.org/conda-forge/win-64/libclang13-18.1.5-default_hf64faad_0.conda
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   name: libcups
   version: 2.3.3
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   size: 1142172
   timestamp: 1686896907750
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   name: libdeflate
   version: '1.20'
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   license_family: BSD
   size: 394383
   timestamp: 1687765514062
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   size: 24183
   timestamp: 1713755271389
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   size: 1442624
   timestamp: 1713755021286
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   timestamp: 1713639388280
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/ukkonen-1.0.1-py311he4fd1f5_4.conda
+  sha256: 384fc81a34e248019d43a115386f77859ab63e0e6f12dade486d76359703743f
+  md5: 5d5ab5c5af32931e03608034f4a5fd75
+  depends:
+  - cffi
+  - libcxx >=15.0.7
+  - python >=3.11,<3.12.0a0
+  - python >=3.11,<3.12.0a0 *_cpython
+  - python_abi 3.11.* *_cp311
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/ukkonen
+  size: 13958
+  timestamp: 1695549884615
 - kind: conda
   name: urllib3
   version: 2.2.1
@@ -8017,6 +10928,26 @@ packages:
   license_family: Proprietary
   size: 749868
   timestamp: 1702511239004
+- kind: conda
+  name: virtualenv
+  version: 20.26.2
+  build: pyhd8ed1ab_0
+  subdir: noarch
+  noarch: python
+  url: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.26.2-pyhd8ed1ab_0.conda
+  sha256: 1eefd180723fb2fd295352323b53777eeae5765b24d62ae75fc9f1e71b455f11
+  md5: 7d36e7a485ea2f5829408813bdbbfb38
+  depends:
+  - distlib <1,>=0.3.7
+  - filelock <4,>=3.12.2
+  - platformdirs <5,>=3.9.1
+  - python >=3.8
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/virtualenv
+  size: 3458445
+  timestamp: 1715681264937
 - kind: conda
   name: vs2015_runtime
   version: 14.38.33130
@@ -8458,6 +11389,63 @@ packages:
   license: LGPL-2.1 and GPL-2.0
   size: 217804
   timestamp: 1660346976440
+- kind: conda
+  name: yaml
+  version: 0.2.5
+  build: h0d85af4_2
+  build_number: 2
+  subdir: osx-64
+  url: https://conda.anaconda.org/conda-forge/osx-64/yaml-0.2.5-h0d85af4_2.tar.bz2
+  sha256: 5301417e2c8dea45b401ffee8df3957d2447d4ce80c83c5ff151fc6bfe1c4148
+  md5: d7e08fcf8259d742156188e8762b4d20
+  license: MIT
+  license_family: MIT
+  size: 84237
+  timestamp: 1641347062780
+- kind: conda
+  name: yaml
+  version: 0.2.5
+  build: h3422bc3_2
+  build_number: 2
+  subdir: osx-arm64
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h3422bc3_2.tar.bz2
+  sha256: 93181a04ba8cfecfdfb162fc958436d868cc37db504c58078eab4c1a3e57fbb7
+  md5: 4bb3f014845110883a3c5ee811fd84b4
+  license: MIT
+  license_family: MIT
+  size: 88016
+  timestamp: 1641347076660
+- kind: conda
+  name: yaml
+  version: 0.2.5
+  build: h7f98852_2
+  build_number: 2
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
+  sha256: a4e34c710eeb26945bdbdaba82d3d74f60a78f54a874ec10d373811a5d217535
+  md5: 4cb3ad778ec2d5a7acbdf254eb1c42ae
+  depends:
+  - libgcc-ng >=9.4.0
+  license: MIT
+  license_family: MIT
+  size: 89141
+  timestamp: 1641346969816
+- kind: conda
+  name: yaml
+  version: 0.2.5
+  build: h8ffe710_2
+  build_number: 2
+  subdir: win-64
+  url: https://conda.anaconda.org/conda-forge/win-64/yaml-0.2.5-h8ffe710_2.tar.bz2
+  sha256: 4e2246383003acbad9682c7c63178e2e715ad0eb84f03a8df1fbfba455dfedc5
+  md5: adbfb9f45d1004a26763652246a33764
+  depends:
+  - vc >=14.1,<15.0a0
+  - vs2015_runtime >=14.16.27012
+  license: MIT
+  license_family: MIT
+  size: 63274
+  timestamp: 1641347623319
 - kind: conda
   name: zipp
   version: 3.17.0
@@ -8552,3 +11540,66 @@ packages:
   license_family: BSD
   size: 545199
   timestamp: 1693151163452
+- kind: conda
+  name: zstd
+  version: 1.5.6
+  build: h0ea2cb4_0
+  subdir: win-64
+  url: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.6-h0ea2cb4_0.conda
+  sha256: 768e30dc513568491818fb068ee867c57c514b553915536da09e5d10b4ebf3c3
+  md5: 9a17230f95733c04dc40a2b1e5491d74
+  depends:
+  - libzlib >=1.2.13,<1.3.0a0
+  - ucrt >=10.0.20348.0
+  - vc >=14.2,<15
+  - vc14_runtime >=14.29.30139
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 349143
+  timestamp: 1714723445995
+- kind: conda
+  name: zstd
+  version: 1.5.6
+  build: h915ae27_0
+  subdir: osx-64
+  url: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
+  sha256: efa04a98cb149643fa54c4dad5a0179e36a5fbc88427ea0eec88ceed87fd0f96
+  md5: 4cb2cd56f039b129bb0e491c1164167e
+  depends:
+  - __osx >=10.9
+  - libzlib >=1.2.13,<1.3.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 498900
+  timestamp: 1714723303098
+- kind: conda
+  name: zstd
+  version: 1.5.6
+  build: ha6fb4c9_0
+  subdir: linux-64
+  url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
+  sha256: c558b9cc01d9c1444031bd1ce4b9cff86f9085765f17627a6cd85fc623c8a02b
+  md5: 4d056880988120e29d75bfff282e0f45
+  depends:
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+  - libzlib >=1.2.13,<1.3.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 554846
+  timestamp: 1714722996770
+- kind: conda
+  name: zstd
+  version: 1.5.6
+  build: hb46c0d2_0
+  subdir: osx-arm64
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda
+  sha256: 2d4fd1ff7ee79cd954ca8e81abf11d9d49954dd1fef80f27289e2402ae9c2e09
+  md5: d96942c06c3e84bfcc5efb038724a7fd
+  depends:
+  - __osx >=11.0
+  - libzlib >=1.2.13,<1.3.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 405089
+  timestamp: 1714723101397
diff --git a/pyproject.toml b/pyproject.toml
index 25e51ab..353eb50 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,6 +49,7 @@ skltemplate = { path=".", editable=true }
 [tool.pixi.feature.lint.dependencies]
 # The version below should be aligned with the one of `.pre-commit-config.yaml`
 black = "23.3.0"
+pre-commit = "3.7.1"
 ruff = "0.4.2"
 
 [tool.pixi.feature.lint.tasks]
@@ -81,6 +82,7 @@ clean-doc = { cmd = "rm -rf _build", cwd = "doc" }
 doc = ["doc"]
 lint = ["lint"]
 test = ["test"]
+dev = ["doc", "lint", "test"]
 
 [tool.black]
 line-length = 88