From dcfaf1b1d33c7463dc0c78fa5b74e0c1cee09133 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Tue, 28 Dec 2021 19:11:24 -0700 Subject: [PATCH 01/30] add dependency missing from pip version of xdesign --- examples/examples_requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/examples/examples_requirements.txt b/examples/examples_requirements.txt index 9dfa3cce2..c76f94e24 100644 --- a/examples/examples_requirements.txt +++ b/examples/examples_requirements.txt @@ -1,4 +1,5 @@ astra-toolbox +cached_property colour_demosaicing xdesign ray[tune] From e9ff99e3a736a8922df97e8203ed38417a4c947f Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Tue, 28 Dec 2021 19:31:23 -0700 Subject: [PATCH 02/30] update example command for GPU install --- docs/source/install.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/install.rst b/docs/source/install.rst index 3e7fff1f2..2941b6913 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -54,7 +54,7 @@ The instructions above install a CPU-only version of SCICO. To install a version :: - pip install --upgrade "jaxlib==0.1.70+cuda110" -f https://storage.googleapis.com/jax-releases/jax_releases.html + pip install --upgrade "jaxlib==0.1.75+cuda110" -f https://storage.googleapis.com/jax-releases/jax_releases.html From ad6bb4d53886cf954c491502579419cab997f892 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Tue, 28 Dec 2021 19:45:13 -0700 Subject: [PATCH 03/30] add dev requirements --- docs/source/contributing.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 6fb808180..db76ed961 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -77,6 +77,7 @@ Installing a Development Version :: pip install -r requirements.txt # Installs basic requirements + pip install -r dev_requirements.txt # Installs developer requirements pip install -r docs/docs_requirements.txt # Installs documentation requirements pip install -r examples/examples_requirements.txt # Installs example requirements pip install -e . # Installs SCICO from the current directory in editable mode From 4ba2057a57609bdff5acdd41b8b735b39bf36548 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Tue, 28 Dec 2021 19:59:21 -0700 Subject: [PATCH 04/30] fix bug in link --- examples/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/README.rst b/examples/README.rst index 54766aa72..99c04efe0 100644 --- a/examples/README.rst +++ b/examples/README.rst @@ -37,7 +37,7 @@ A number of files in this directory assist in the mangement of the usage example `examples_requirements.txt `_ Requirements file (as used by ``pip``) listing additional dependencies for running the usage example scripts. -`notebooks_requirements.txt `_ +`notebooks_requirements.txt `_ Requirements file (as used by ``pip``) listing additional dependencies for building the Jupyter notebooks from the usage example scripts. `makenotebooks.py `_ From f8d072e6b87c033f6e82006e1282cf024ff779bd Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 29 Dec 2021 17:48:09 -0700 Subject: [PATCH 05/30] fix incorrect instruction for astra --- docs/source/contributing.rst | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index db76ed961..d7e411b94 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -79,9 +79,14 @@ Installing a Development Version pip install -r requirements.txt # Installs basic requirements pip install -r dev_requirements.txt # Installs developer requirements pip install -r docs/docs_requirements.txt # Installs documentation requirements - pip install -r examples/examples_requirements.txt # Installs example requirements pip install -e . # Installs SCICO from the current directory in editable mode + Pip should be used to install the extra requirements for running examples except astra which should be installed via conda: + + :: + conda install -c astra-toolbox/label/dev astra-toolbox + pip install -r examples/examples_requirements.txt # Installs other example requirements + 9. The SCICO project uses the `black `_, `isort `_ and `pylint `_ From bbca3959bd4c2546152c90c47ff109e688a41e63 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 29 Dec 2021 18:31:38 -0700 Subject: [PATCH 06/30] Doc fix --- docs/source/contributing.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index d7e411b94..5573e9de9 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -84,6 +84,7 @@ Installing a Development Version Pip should be used to install the extra requirements for running examples except astra which should be installed via conda: :: + conda install -c astra-toolbox/label/dev astra-toolbox pip install -r examples/examples_requirements.txt # Installs other example requirements From 289dd386730f909274d2d09c3772acd087a18ecf Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 19:18:57 -0700 Subject: [PATCH 07/30] move docs building instructions from install to contributing --- docs/source/contributing.rst | 19 ++++++++++++++++++- docs/source/install.rst | 26 -------------------------- 2 files changed, 18 insertions(+), 27 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 5573e9de9..1a1a74e45 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -397,8 +397,25 @@ scico-data repositories must be updated and kept in sync. Building Documentation ---------------------- -To build a local copy of the docs, from the repo root directory, do +A local copy of the documentation can be built from the respository root directory by doing :: python setup.py build_sphinx + + +Alternatively: + +1. Navigate to the docs directory ``docs/`` + +2. Install dependencies + + :: + + pip install -r docs_requirements.txt + +3. Build documentation + + :: + + make html diff --git a/docs/source/install.rst b/docs/source/install.rst index 2941b6913..9a299a87c 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -81,29 +81,3 @@ For Developers For installing a version of SCICO suitable for development, see the instructions in :ref:`scico_dev_contributing`. - - -Building Documentation ----------------------- - -The documentation can be built from the respository root directory by doing - -:: - - python setup.py build_sphinx - -Alternatively: - -1. Navigate to the docs directory ``docs/`` - -2. Install dependencies - - :: - - pip install -r docs_requirements.txt - -3. Build documentation - - :: - - make html From 462af6dea68dd79cc3371bfadc28b16e234758f2 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 20:13:09 -0700 Subject: [PATCH 08/30] Update astra install channel --- docs/source/contributing.rst | 2 +- docs/source/install.rst | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 1a1a74e45..75bf65a30 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -85,7 +85,7 @@ Installing a Development Version :: - conda install -c astra-toolbox/label/dev astra-toolbox + conda install -c astra-toolbox astra-toolbox pip install -r examples/examples_requirements.txt # Installs other example requirements diff --git a/docs/source/install.rst b/docs/source/install.rst index 9a299a87c..6c49b8a7b 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -61,13 +61,11 @@ The instructions above install a CPU-only version of SCICO. To install a version Additional Dependencies ----------------------- -We use the `ASTRA Toolbox `_ for tomographic projectors. We currently require the development version of ASTRA, as suggested by the package maintainers. - -The development version of ASTRA can be installed using conda: +We use the `ASTRA Toolbox `_ for tomographic projectors. `ASTRA Toolbox` can be installed using conda by running: :: - conda install -c astra-toolbox/label/dev astra-toolbox + conda install -c astra-toolbox astra-toolbox Alternatively, it can be `built from source `_. From 21e0f4105ff416aed901d94f9dc2c8032b39c7a0 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 22:08:17 -0700 Subject: [PATCH 09/30] add dependency installation in examples --- docs/source/examples.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 1729dfbdd..e926ba9ca 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -6,6 +6,15 @@ Usage Examples .. toctree:: :maxdepth: 1 +Some examples may use additional dependecies. These dependencies are listed in `examples_requirements.txt `. +Pip should be used to install these extra requirements except astra which should be installed via conda: + + :: + + conda install -c astra-toolbox astra-toolbox + pip install -r examples/examples_requirements.txt # Installs other example requirements + +The dependencies can also be installed one by one as required. Organized by Application ------------------------ From 3c4e867961734dd582a910fa2df0144ac5b8d238 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 22:15:33 -0700 Subject: [PATCH 10/30] fix link --- docs/source/examples.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index e926ba9ca..eb04dce34 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -6,7 +6,7 @@ Usage Examples .. toctree:: :maxdepth: 1 -Some examples may use additional dependecies. These dependencies are listed in `examples_requirements.txt `. +Some examples may use additional dependecies. These dependencies are listed in `examples_requirements.txt `_. Pip should be used to install these extra requirements except astra which should be installed via conda: :: From 06f7b2c70bf2ad51bb80f46a99e0f2dd786e751d Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 22:23:46 -0700 Subject: [PATCH 11/30] add example dependencies heading --- docs/source/examples.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index eb04dce34..8dabddb8a 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -6,6 +6,9 @@ Usage Examples .. toctree:: :maxdepth: 1 +Example Dependencies +------------------------ + Some examples may use additional dependecies. These dependencies are listed in `examples_requirements.txt `_. Pip should be used to install these extra requirements except astra which should be installed via conda: From 393c5a1c798e5ed2a40ebb10ac2e4c0888e276a1 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 23:21:18 -0700 Subject: [PATCH 12/30] add ref --- docs/source/contributing.rst | 2 ++ docs/source/examples.rst | 1 + 2 files changed, 3 insertions(+) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 75bf65a30..317278ed3 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -88,6 +88,8 @@ Installing a Development Version conda install -c astra-toolbox astra-toolbox pip install -r examples/examples_requirements.txt # Installs other example requirements + See :ref:`_example_dependencies`. + 9. The SCICO project uses the `black `_, `isort `_ and `pylint `_ diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 8dabddb8a..f77fb0cbc 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -6,6 +6,7 @@ Usage Examples .. toctree:: :maxdepth: 1 +.. _example_dependencies: Example Dependencies ------------------------ From d4be3b7fbd486ef75650f6884e9945246e6a0e29 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 23:45:40 -0700 Subject: [PATCH 13/30] add new ref --- docs/source/contributing.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 317278ed3..d9cddfabe 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -89,6 +89,7 @@ Installing a Development Version pip install -r examples/examples_requirements.txt # Installs other example requirements See :ref:`_example_dependencies`. + See :ref:`_example_notebooks`. 9. The SCICO project uses the `black `_, From ec83acc016008fe1df34a41ab22167e7f465b3be Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Mon, 3 Jan 2022 23:58:05 -0700 Subject: [PATCH 14/30] update links --- docs/source/contributing.rst | 4 ++-- docs/source/install.rst | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index d9cddfabe..5c04b5e7e 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -88,8 +88,8 @@ Installing a Development Version conda install -c astra-toolbox astra-toolbox pip install -r examples/examples_requirements.txt # Installs other example requirements - See :ref:`_example_dependencies`. - See :ref:`_example_notebooks`. + See :ref:`example_dependencies`. + See :ref:`example_notebooks`. 9. The SCICO project uses the `black `_, diff --git a/docs/source/install.rst b/docs/source/install.rst index 6c49b8a7b..874f271a2 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -78,4 +78,4 @@ For Developers -------------- For installing a version of SCICO suitable for development, -see the instructions in :ref:`scico_dev_contributing`. +see the instructions in :ref:`scico_dev_contributing`. Also see :ref:`example_dependencies`. From 410309116ee2fb05e3d9878fa29cc7303562c27a Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Tue, 4 Jan 2022 00:06:50 -0700 Subject: [PATCH 15/30] clean up links --- docs/source/contributing.rst | 9 +-------- docs/source/install.rst | 2 +- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 5c04b5e7e..0790a0af3 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -81,15 +81,8 @@ Installing a Development Version pip install -r docs/docs_requirements.txt # Installs documentation requirements pip install -e . # Installs SCICO from the current directory in editable mode - Pip should be used to install the extra requirements for running examples except astra which should be installed via conda: - :: - - conda install -c astra-toolbox astra-toolbox - pip install -r examples/examples_requirements.txt # Installs other example requirements - - See :ref:`example_dependencies`. - See :ref:`example_notebooks`. + For installing dependencies related to the examples please see :ref:`example_notebooks`. 9. The SCICO project uses the `black `_, diff --git a/docs/source/install.rst b/docs/source/install.rst index 874f271a2..6c49b8a7b 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -78,4 +78,4 @@ For Developers -------------- For installing a version of SCICO suitable for development, -see the instructions in :ref:`scico_dev_contributing`. Also see :ref:`example_dependencies`. +see the instructions in :ref:`scico_dev_contributing`. From 0dde2011e0a48ee5527e49928d23308d037c309c Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Tue, 4 Jan 2022 00:12:47 -0700 Subject: [PATCH 16/30] clean up extra instructions --- docs/source/install.rst | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/docs/source/install.rst b/docs/source/install.rst index 6c49b8a7b..6dd8a7dbc 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -61,17 +61,7 @@ The instructions above install a CPU-only version of SCICO. To install a version Additional Dependencies ----------------------- -We use the `ASTRA Toolbox `_ for tomographic projectors. `ASTRA Toolbox` can be installed using conda by running: - -:: - - conda install -c astra-toolbox astra-toolbox - -Alternatively, it can be `built from source `_. - -We also support the `Super-Voxel Model-Based Iterative Reconstruction `_ package as an alternative tomographic projector. Since this package can be installed via ``pip``, it is -included in the list of package dependencies (``requirements.txt``), and need -not be separately installed. +For installing dependencies related to the examples please see :ref:`example_notebooks`. For Developers From 36beca905d775a68513b906e7111ebfa4a85d78a Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 5 Jan 2022 20:10:07 -0700 Subject: [PATCH 17/30] Fix wording --- docs/source/contributing.rst | 52 +++++++++++++++++------------------- 1 file changed, 25 insertions(+), 27 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index a3fdb92c8..6aaf32ff3 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -194,6 +194,31 @@ A feature development workflow might look like this: 11. Delete the branch after it has been merged. + +Building Documentation +---------------------- + +Before building the documentation, one must install the documentation specific dependencies by running + + :: + + pip install -r docs_requirements.txt + + +Then, a local copy of the documentation can be built from the respository root directory by running + +:: + + python setup.py build_sphinx + + +Alternatively, one can also build the documentation by running the following from the `docs/`` directory + + :: + + make html + + Adding Data ----------- @@ -402,30 +427,3 @@ and ``scico-data`` repositories must be updated and kept in sync. :: git submodule foreach --recursive 'git push' && git push - - -Building Documentation ----------------------- - -A local copy of the documentation can be built from the respository root directory by doing - -:: - - python setup.py build_sphinx - - -Alternatively: - -1. Navigate to the docs directory ``docs/`` - -2. Install dependencies - - :: - - pip install -r docs_requirements.txt - -3. Build documentation - - :: - - make html From b4f0cd31421bd12d46f179e9283cef596612d55c Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 5 Jan 2022 20:43:01 -0700 Subject: [PATCH 18/30] fix indentation: --- docs/source/contributing.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 6aaf32ff3..6fcc4a2e7 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -207,9 +207,9 @@ Before building the documentation, one must install the documentation specific d Then, a local copy of the documentation can be built from the respository root directory by running -:: + :: - python setup.py build_sphinx + python setup.py build_sphinx Alternatively, one can also build the documentation by running the following from the `docs/`` directory From e278182ecfe7d0442539c8eb953fdd3c95154189 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 5 Jan 2022 21:01:47 -0700 Subject: [PATCH 19/30] revert --- docs/source/contributing.rst | 52 +++++++++++++++++++----------------- 1 file changed, 27 insertions(+), 25 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 6fcc4a2e7..a3fdb92c8 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -194,31 +194,6 @@ A feature development workflow might look like this: 11. Delete the branch after it has been merged. - -Building Documentation ----------------------- - -Before building the documentation, one must install the documentation specific dependencies by running - - :: - - pip install -r docs_requirements.txt - - -Then, a local copy of the documentation can be built from the respository root directory by running - - :: - - python setup.py build_sphinx - - -Alternatively, one can also build the documentation by running the following from the `docs/`` directory - - :: - - make html - - Adding Data ----------- @@ -427,3 +402,30 @@ and ``scico-data`` repositories must be updated and kept in sync. :: git submodule foreach --recursive 'git push' && git push + + +Building Documentation +---------------------- + +A local copy of the documentation can be built from the respository root directory by doing + +:: + + python setup.py build_sphinx + + +Alternatively: + +1. Navigate to the docs directory ``docs/`` + +2. Install dependencies + + :: + + pip install -r docs_requirements.txt + +3. Build documentation + + :: + + make html From 3805e4ec9578996023a4a225c774880bcf2fa918 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 5 Jan 2022 21:23:00 -0700 Subject: [PATCH 20/30] remove doc duplication --- docs/source/contributing.rst | 46 ++++++++++++++---------------------- 1 file changed, 18 insertions(+), 28 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index a3fdb92c8..edc877e40 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -107,13 +107,30 @@ Installing a Development Version Building Documentation ---------------------- -To build a local copy of the docs, from the repo root directory, do +A local copy of the documentation can be built from the respository root directory by doing :: python setup.py build_sphinx +Alternatively: + +1. Navigate to the docs directory ``docs/`` + +2. Install dependencies + + :: + + pip install -r docs_requirements.txt + +3. Build documentation + + :: + + make html + + Contributing Code ----------------- @@ -402,30 +419,3 @@ and ``scico-data`` repositories must be updated and kept in sync. :: git submodule foreach --recursive 'git push' && git push - - -Building Documentation ----------------------- - -A local copy of the documentation can be built from the respository root directory by doing - -:: - - python setup.py build_sphinx - - -Alternatively: - -1. Navigate to the docs directory ``docs/`` - -2. Install dependencies - - :: - - pip install -r docs_requirements.txt - -3. Build documentation - - :: - - make html From 4bc20c4c7f2a39c55c69873673724eb241cfa64b Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Wed, 5 Jan 2022 22:13:16 -0700 Subject: [PATCH 21/30] misc changes --- docs/source/contributing.rst | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index edc877e40..4b56c5ab4 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -107,28 +107,24 @@ Installing a Development Version Building Documentation ---------------------- -A local copy of the documentation can be built from the respository root directory by doing +Before building the documentation, one must install the documentation specific dependencies by running :: - python setup.py build_sphinx - + pip install -r docs_requirements.txt -Alternatively: +Then, a local copy of the documentation can be built from the respository root directory by running -1. Navigate to the docs directory ``docs/`` - -2. Install dependencies +:: - :: + python setup.py build_sphinx - pip install -r docs_requirements.txt -3. Build documentation +Alternatively, one can also build the documentation by running the following from the `docs/`` directory - :: +:: - make html + make html From 34ff9ac494629fc4b1d8e8a50fae5ba3b8d2ccec Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Thu, 6 Jan 2022 00:21:23 -0700 Subject: [PATCH 22/30] add indent --- docs/source/examples.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index f77fb0cbc..2c0832cb5 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -7,6 +7,7 @@ Usage Examples :maxdepth: 1 .. _example_dependencies: + Example Dependencies ------------------------ From c9ed61a01cfc78d6d2eb1d4cc55d9f15deed51bb Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Thu, 6 Jan 2022 01:48:38 -0700 Subject: [PATCH 23/30] fix typo --- docs/source/contributing.rst | 4 ++-- docs/source/examples.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 4b56c5ab4..4a3bae161 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -58,7 +58,7 @@ Installing a Development Version conda activate scico -6. Navigate to the root of the cloned repository: +6. Change directory to the root of the cloned repository: :: @@ -219,7 +219,7 @@ scico-data repositories must be updated and kept in sync. 1. Add the ``new_data.npz`` file to the ``scico/data`` directory. -2. Navigate to the ``data`` directory and add/commit the new data file: +2. Change directory to the ``data`` directory and add/commit the new data file: :: diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 2c0832cb5..60793d848 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -9,9 +9,9 @@ Usage Examples .. _example_dependencies: Example Dependencies ------------------------- +-------------------- -Some examples may use additional dependecies. These dependencies are listed in `examples_requirements.txt `_. +Some examples use additional dependencies which are listed in `examples_requirements.txt `_. Pip should be used to install these extra requirements except astra which should be installed via conda: :: From cbf811b843b25af474905767b2a7b35212078185 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Thu, 6 Jan 2022 02:04:21 -0700 Subject: [PATCH 24/30] change wording --- docs/source/examples.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 60793d848..0c1a9fc98 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -12,7 +12,7 @@ Example Dependencies -------------------- Some examples use additional dependencies which are listed in `examples_requirements.txt `_. -Pip should be used to install these extra requirements except astra which should be installed via conda: +The additional requirements should be installed via pip, with the exception of astra-toolbox, which should be installed via conda: :: From 6a6b725c3b408063d1a0006d40afff0d679850a1 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Thu, 6 Jan 2022 02:14:10 -0700 Subject: [PATCH 25/30] fix wording --- docs/source/examples.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 0c1a9fc98..67368127b 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -19,7 +19,7 @@ The additional requirements should be installed via pip, with the exception of a conda install -c astra-toolbox astra-toolbox pip install -r examples/examples_requirements.txt # Installs other example requirements -The dependencies can also be installed one by one as required. +The dependencies can also be installed individually as required. Organized by Application ------------------------ From 1ec46141f61bd0159e80bfea7c7ff3060fa98c25 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Thu, 6 Jan 2022 02:19:13 -0700 Subject: [PATCH 26/30] change wording --- docs/source/install.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/install.rst b/docs/source/install.rst index 6dd8a7dbc..066506014 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -61,7 +61,7 @@ The instructions above install a CPU-only version of SCICO. To install a version Additional Dependencies ----------------------- -For installing dependencies related to the examples please see :ref:`example_notebooks`. +For instructions on installing dependencies related to the examples please see :ref:`example_notebooks`. For Developers From 93694fb5721608430cc0cf97005828e3dc07d6ef Mon Sep 17 00:00:00 2001 From: Brendt Wohlberg Date: Thu, 6 Jan 2022 10:28:09 -0700 Subject: [PATCH 27/30] Update examples.rst Address nitpicks. --- docs/source/examples.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 67368127b..5ac2c28a8 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -11,8 +11,9 @@ Usage Examples Example Dependencies -------------------- -Some examples use additional dependencies which are listed in `examples_requirements.txt `_. -The additional requirements should be installed via pip, with the exception of astra-toolbox, which should be installed via conda: +Some examples use additional dependencies, which are listed in `examples_requirements.txt `_. +The additional requirements should be installed via pip, with the exception of ``astra-toolbox``, +which should be installed via conda: :: From 75b666d93ff4da636c9f03a6b16aaaf7db12a1dc Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Fri, 7 Jan 2022 00:02:46 -0700 Subject: [PATCH 28/30] fix bug --- docs/source/contributing.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 4a3bae161..e7b2e2b4e 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -120,7 +120,7 @@ Then, a local copy of the documentation can be built from the respository root d python setup.py build_sphinx -Alternatively, one can also build the documentation by running the following from the `docs/`` directory +Alternatively, one can also build the documentation by running the following from the `docs/` directory :: From 617e993368a1d6bf36e2d62ca4b1d447e024a24a Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Fri, 7 Jan 2022 00:26:26 -0700 Subject: [PATCH 29/30] add comment about neccessity of installing example requirements --- data | 2 +- docs/source/contributing.rst | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/data b/data index ea298a1a1..9e402ca5f 160000 --- a/data +++ b/data @@ -1 +1 @@ -Subproject commit ea298a1a1aeae00beeab4e9f60c124ceaa454bfe +Subproject commit 9e402ca5fe00a01c5629c15d6167fed10b7c46f2 diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index e7b2e2b4e..cfeb2b72b 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -83,6 +83,7 @@ Installing a Development Version For installing dependencies related to the examples please see :ref:`example_notebooks`. + Installing these are neccessary for the successfull running of the tests. 9. The SCICO project uses the `black `_, From d2301b7466e10d7645b9f03675eefe476047a2b7 Mon Sep 17 00:00:00 2001 From: Soumendu Majee Date: Fri, 7 Jan 2022 00:38:35 -0700 Subject: [PATCH 30/30] update submodule --- data | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data b/data index 9e402ca5f..c86c573b8 160000 --- a/data +++ b/data @@ -1 +1 @@ -Subproject commit 9e402ca5fe00a01c5629c15d6167fed10b7c46f2 +Subproject commit c86c573b8a3eee7b0676451c3275d3acc0a7a2d5