From bedb6d10d72f27418d757ba8d0a22d8900c34466 Mon Sep 17 00:00:00 2001 From: David Kastner Date: Tue, 18 Jul 2023 11:11:35 -0400 Subject: [PATCH] Fix docs --- docs/autosummary/qp.analyze.rst | 29 -------------------------- docs/autosummary/qp.plot.rst | 29 -------------------------- docs/autosummary/qp.process.rst | 29 -------------------------- qp/README.md | 15 -------------- qp/__init__.py | 7 ------- qp/cluster/__init__.py | 0 qp/data/README.md | 36 --------------------------------- qp/data/look_and_say.dat | 15 -------------- qp/setup/__init__.py | 0 qp/structure/__init__.py | 0 10 files changed, 160 deletions(-) delete mode 100644 docs/autosummary/qp.analyze.rst delete mode 100644 docs/autosummary/qp.plot.rst delete mode 100644 docs/autosummary/qp.process.rst delete mode 100644 qp/README.md create mode 100644 qp/cluster/__init__.py delete mode 100644 qp/data/README.md delete mode 100644 qp/data/look_and_say.dat create mode 100644 qp/setup/__init__.py create mode 100644 qp/structure/__init__.py diff --git a/docs/autosummary/qp.analyze.rst b/docs/autosummary/qp.analyze.rst deleted file mode 100644 index 5f15e2a..0000000 --- a/docs/autosummary/qp.analyze.rst +++ /dev/null @@ -1,29 +0,0 @@ -qp.analyze -========== - -.. automodule:: qp.analyze - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - canvas - - - - - - - - - - - - - diff --git a/docs/autosummary/qp.plot.rst b/docs/autosummary/qp.plot.rst deleted file mode 100644 index 30c8521..0000000 --- a/docs/autosummary/qp.plot.rst +++ /dev/null @@ -1,29 +0,0 @@ -qp.plot -======= - -.. automodule:: qp.plot - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - format_plot - - - - - - - - - - - - - diff --git a/docs/autosummary/qp.process.rst b/docs/autosummary/qp.process.rst deleted file mode 100644 index fd6bb17..0000000 --- a/docs/autosummary/qp.process.rst +++ /dev/null @@ -1,29 +0,0 @@ -qp.process -========== - -.. automodule:: qp.process - - - - - - - - .. rubric:: Functions - - .. autosummary:: - - canvas - - - - - - - - - - - - - diff --git a/qp/README.md b/qp/README.md deleted file mode 100644 index e080984..0000000 --- a/qp/README.md +++ /dev/null @@ -1,15 +0,0 @@ -QuantumPDB -============================== - -## 1. What is included? -### File structure -``` -. -|── cli.py # Command-line interface entry point -├── docs # Readthedocs documentation site -├── qp # Directory containing the quantumPDB modules -│ ├── process # Processes protein structures -│ ├── analyze # Analysis of electronic structure calculations -│ └── plot # Generalizable plotting and vizualization -└── ... -``` \ No newline at end of file diff --git a/qp/__init__.py b/qp/__init__.py index 7b9587a..e69de29 100644 --- a/qp/__init__.py +++ b/qp/__init__.py @@ -1,7 +0,0 @@ -"""Workflow for generate a database of proteins with quantum properties""" - -# Add imports here -from .process import * - - -from ._version import __version__ diff --git a/qp/cluster/__init__.py b/qp/cluster/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/qp/data/README.md b/qp/data/README.md deleted file mode 100644 index 5301dae..0000000 --- a/qp/data/README.md +++ /dev/null @@ -1,36 +0,0 @@ -# Sample Package Data - -This directory contains sample additional data you may want to include with your package. -This is a place where non-code related additional information (such as data files, molecular structures, etc.) can -go that you want to ship alongside your code. - -Please note that it is not recommended to place large files in your git directory. If your project requires files larger -than a few megabytes in size it is recommended to host these files elsewhere. This is especially true for binary files -as the `git` structure is unable to correctly take updates to these files and will store a complete copy of every version -in your `git` history which can quickly add up. As a note most `git` hosting services like GitHub have a 1 GB per repository -cap. - -## Including package data - -Modify your package's `pyproject.toml` file. -Update the [tool.setuptools.package_data](https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data) -and point it at the correct files. -Paths are relative to `package_dir`. - -Package data can be accessed at run time with `importlib.resources` or the `importlib_resources` back port. -See https://setuptools.pypa.io/en/latest/userguide/datafiles.html#accessing-data-files-at-runtime -for suggestions. - -If modules within your package will access internal data files using -[the recommended approach](https://setuptools.pypa.io/en/latest/userguide/datafiles.html#accessing-data-files-at-runtime), -you may need to include `importlib_resources` in your package dependencies. -In `pyproject.toml`, include the following in your `[project]` table. -``` -dependencies = [ - "importlib-resources;python_version<'3.10'", -] -``` - -## Manifest - -* `look_and_say.dat`: first entries of the "Look and Say" integer series, sequence [A005150](https://oeis.org/A005150) diff --git a/qp/data/look_and_say.dat b/qp/data/look_and_say.dat deleted file mode 100644 index 97df452..0000000 --- a/qp/data/look_and_say.dat +++ /dev/null @@ -1,15 +0,0 @@ -1 -11 -21 -1211 -111221 -312211 -13112221 -1113213211 -31131211131221 -13211311123113112211 -11131221133112132113212221 -3113112221232112111312211312113211 -1321132132111213122112311311222113111221131221 -11131221131211131231121113112221121321132132211331222113112211 -311311222113111231131112132112311321322112111312211312111322212311322113212221 \ No newline at end of file diff --git a/qp/setup/__init__.py b/qp/setup/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/qp/structure/__init__.py b/qp/structure/__init__.py new file mode 100644 index 0000000..e69de29