From 67f7e8290c037d68df46add31ddb1f46711f3219 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 1 Apr 2025 12:42:33 -0700 Subject: [PATCH 1/2] moving under the hood to the user guide --- docs/cookbook/index.rst | 1 - docs/guide/index.rst | 1 + docs/guide/introduction.rst | 2 ++ docs/{cookbook => guide}/under_the_hood.rst | 0 4 files changed, 3 insertions(+), 1 deletion(-) rename docs/{cookbook => guide}/under_the_hood.rst (100%) diff --git a/docs/cookbook/index.rst b/docs/cookbook/index.rst index 01bb0f1ab..30ba7b591 100644 --- a/docs/cookbook/index.rst +++ b/docs/cookbook/index.rst @@ -160,7 +160,6 @@ List of Cookbooks hand_write_ligand_network ligandnetwork_vis create_alchemical_network - under_the_hood user_charges bespoke_parameters diff --git a/docs/guide/index.rst b/docs/guide/index.rst index 10eec0531..8399cc65c 100644 --- a/docs/guide/index.rst +++ b/docs/guide/index.rst @@ -9,4 +9,5 @@ User Guide results/index cli/index protocols/index + under_the_hood troubleshooting diff --git a/docs/guide/introduction.rst b/docs/guide/introduction.rst index b1ec8eb73..d74486560 100644 --- a/docs/guide/introduction.rst +++ b/docs/guide/introduction.rst @@ -43,6 +43,8 @@ calculate that :math:`\Delta G`. The :ref:`gather results ` stage aggregates the individual results for further analysis. For example, the CLI's ``gather`` command will create a table of the :math:`\Delta G` for each leg. +For more workflow details, see :ref:`under-the-hood`. + .. TODO: Should the CLI workflow be moved to under "CLI Interface"? CLI Workflow diff --git a/docs/cookbook/under_the_hood.rst b/docs/guide/under_the_hood.rst similarity index 100% rename from docs/cookbook/under_the_hood.rst rename to docs/guide/under_the_hood.rst From d91e3d22628af8210113563070258faf09b05580 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 1 Apr 2025 14:27:08 -0700 Subject: [PATCH 2/2] adding pip to docs env dependencies --- docs/environment.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/environment.yaml b/docs/environment.yaml index 054595d51..aaaa2e8d5 100644 --- a/docs/environment.yaml +++ b/docs/environment.yaml @@ -16,6 +16,7 @@ dependencies: - openff-units - openmm - packaging +- pip - plugcli - python=3.10 - sphinx <7.3