From 3d05b5dcf27f90eba6e167d5d4b46b6998b92a6d Mon Sep 17 00:00:00 2001 From: rarhin711 Date: Mon, 16 Sep 2024 13:13:32 -0400 Subject: [PATCH 1/2] changes in gallery and video rsts --- doc/conf.py | 2 +- doc/gallery.rst | 22 ++++++++++----------- doc/gallery_ref.rst | 28 --------------------------- doc/tutorials.rst | 37 ++++++++++++++++++++++++++--------- doc/video_ref.rst | 47 --------------------------------------------- 5 files changed, 39 insertions(+), 97 deletions(-) delete mode 100644 doc/gallery_ref.rst delete mode 100644 doc/video_ref.rst diff --git a/doc/conf.py b/doc/conf.py index c7ed294f..74331a8d 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -31,7 +31,7 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme' + 'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme', 'sphinx_panels', ] # Add any paths that contain templates here, relative to this directory. diff --git a/doc/gallery.rst b/doc/gallery.rst index f80415b0..b41b5a52 100644 --- a/doc/gallery.rst +++ b/doc/gallery.rst @@ -7,26 +7,24 @@ EFP gallery Gallery ======= -This gallery highlights the use of EFP to bridge the gap between chemistry, biology, and physics, -particularly in solving real-world challenges in drug design and photosynthesis. EFP plays a crucial -role in understanding and optimizing these complex processes by providing detailed insights into +This gallery highlights the use of EFP to bridge the gap between chemistry, biology, and physics, +particularly in solving real-world challenges in drug design and photosynthesis. EFP plays a crucial +role in understanding and optimizing these complex processes by providing detailed insights into molecular interactions. -.. _Drug-design: https://www.drug_design.com -Drug-design_ -^^^^^^^^^^^^ -.. _Drug-design: https://www.drug_design.com +:ref:`Drug-design` +^^^^^^^^^^^^^^^^^^ + .. image:: ../images/drug_design.png - :target: https://www.drug_design.com :alt: Drug design :width: 300 -.. _Photosynthesis: file:///C:/Users/richm/libefp2.github.io/html/gallery_ref.html -Photosynthesis_ -^^^^^^^^^^^^^^^ + +:ref:`Photosynthesis` +^^^^^^^^^^^^^^^^^^^^^ .. image:: ../images/photo.png - :target: file:///C:/Users/richm/libefp2.github.io/html/gallery_ref.html :alt: Photosynthesis :width: 300 + diff --git a/doc/gallery_ref.rst b/doc/gallery_ref.rst deleted file mode 100644 index fed49407..00000000 --- a/doc/gallery_ref.rst +++ /dev/null @@ -1,28 +0,0 @@ -.. _gallery_images: - -************** -Photosynthesis -************** - -Fenna-Matthews-Olson (FMO) complex -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -FMO monomer pigments - -.. ../image:: images/FMO_mon_pigs.bmp - :width: 300 - -FMO trimer bacteriochlorophylls - -.. ../image:: images/FMO_trimer_BCLs.bmp - :width: 300 - -FMO trimer pigments - -.. ../image:: images/FMO_trimer_pigs.bmp - :width: 300 - -FMO waters within 15 Angstroms - -.. ../image:: images/FMO_waters15a.bmp - :width: 300 diff --git a/doc/tutorials.rst b/doc/tutorials.rst index a9dbbef8..56900384 100644 --- a/doc/tutorials.rst +++ b/doc/tutorials.rst @@ -11,16 +11,35 @@ This section deals with running an EFP job on a non-covalently bonded system. The steps to running an EFP calculation on a system are: -* Running MAKEFP job in software package GAMESS [1_] -* Obtaining EFP parameters from MAKEFP output [1_] -* Preparing LIBEFP input file [2_] -* Running EFP calculation in LIBEFP [2_] +.. dropdown:: Running MAKEFP job in software package GAMESS + This is explicitly shown in :ref:`parameters` -.. _1: file:///C:/Users/richm/libefp2.github.io/html/parameters.html -.. _2: file:///C:/Users/richm/libefp2.github.io/html/libefp_ref.html +.. dropdown:: Obtaining EFP parameters from MAKEFP output -Videos_ -^^^^^^^ -.. _Videos: file:///C:/Users/richm/libefp2.github.io/html/video_ref.html + Refer to :ref:`parameters` + +.. dropdown:: Preparing LIBEFP input file + + Refer to :ref:`running efp calculations` + +.. dropdown:: Running EFP calculation in LIBEFP + + Refer to :ref:`running efp calculations` + + + + +Videos +~~~~~~ + +.. dropdown:: See links to videos + + `How to run MAKEFP job `_ + + `How to submit MAKEFP input in GAMESS `_ + + `Analyzing MAKEFP output `_ + + `Obtaining EFP parameters and running EFP calculations in LIBEFP `_ diff --git a/doc/video_ref.rst b/doc/video_ref.rst deleted file mode 100644 index 14fcaf1a..00000000 --- a/doc/video_ref.rst +++ /dev/null @@ -1,47 +0,0 @@ -.. _video: - -*************** -Video Tutorials -*************** - -Preparing the EFP input file -============================ - -.. raw:: html - - - - - -Submiting the EFP job -===================== - -.. raw:: html - - - - - -Viewing output -============== -.. raw:: html - - - - - -Running an EFP Calculation -========================== - -.. raw:: html - - - From 6161d991ab9964491005f67d88188545ce913397 Mon Sep 17 00:00:00 2001 From: Jacklaw441 <74787968+Jacklaw441@users.noreply.github.com> Date: Mon, 16 Sep 2024 15:55:10 -0400 Subject: [PATCH 2/2] Update documentation.yml I am not Richmond, but it's his branch --- .github/workflows/documentation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 54f003c9..e9d22619 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -13,7 +13,7 @@ jobs: - uses: actions/setup-python@v5 - name: Install dependencies run: | - pip install sphinx sphinx_rtd_theme myst_parser + pip install sphinx sphinx_rtd_theme myst_parser sphinx_panels - name: Sphinx build run: | sphinx-build doc _build