From 54c41fed035d19df4c5c70ed2f5eee027b541449 Mon Sep 17 00:00:00 2001
From: vicpaton <victor.paton@outlook.com>
Date: Mon, 17 Jun 2024 15:27:03 +0200
Subject: [PATCH] added initial api page

---
 docs/source/api.rst           | 16 ++++++++++
 docs/source/developer_docs.md | 58 -----------------------------------
 2 files changed, 16 insertions(+), 58 deletions(-)
 create mode 100644 docs/source/api.rst
 delete mode 100644 docs/source/developer_docs.md

diff --git a/docs/source/api.rst b/docs/source/api.rst
new file mode 100644
index 0000000..fb5abfc
--- /dev/null
+++ b/docs/source/api.rst
@@ -0,0 +1,16 @@
+API
+===
+.. module:: networkcommons
+.. automodule:: networkcommons
+   :noindex:
+   
+Import networkcommons as::
+
+   import networkcommons as nc
+
+Data reprocessing:
+--------------
+.. autosummary::
+   :toctree: generated
+
+   run_deseq2
diff --git a/docs/source/developer_docs.md b/docs/source/developer_docs.md
deleted file mode 100644
index 3017a37..0000000
--- a/docs/source/developer_docs.md
+++ /dev/null
@@ -1,58 +0,0 @@
-## Pre-commit documentation
-
-[Pre-commit](https://pre-commit.com/) checks are fast programs that
-check code for errors, inconsistencies and code styles, before the code
-is committed. This is a brief documentation of pre-commits checks
-pre-sets in the scverse-template.
-
-The following pre-commit checks for code style and format.
-
--   [black](https://black.readthedocs.io/en/stable/): standard code
-    formatter in Python.
--   [autopep8](https://github.com/hhatto/autopep8): code formatter to
-    conform to [PEP8](https://peps.python.org/pep-0008/) style guide.
--   [isort](https://pycqa.github.io/isort/): sort module imports into
-    sections and types.
--   [prettier](https://prettier.io/docs/en/index.html): standard code
-    formatter for non-Python files (e.g. YAML).
--   [blacken-docs](https://github.com/asottile/blacken-docs): black on
-    python code in docs.
-
-The following pre-commit checks for errors, inconsistencies and typing.
-
--   [flake8](https://flake8.pycqa.org/en/latest/): standard check for errors in Python files.
-    -   [flake8-tidy-imports](https://github.com/adamchainz/flake8-tidy-imports):
-        tidy module imports.
-    -   [flake8-docstrings](https://github.com/PyCQA/flake8-docstrings):
-        pydocstyle extension of flake8.
-    -   [flake8-rst-docstrings](https://github.com/peterjc/e8-rst-docstrings):
-        extension of `flake8-docstrings` for `rst` docs.
-    -   [flake8-comprehensions](https://github.com/adamchainz/e8-comprehensions):
-        write better list/set/dict comprehensions.
-    -   [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear):
-        find possible bugs and design issues in program.
-    -   [flake8-blind-except](https://github.com/elijahandrews/flake8-blind-except):
-        checks for blind, catch-all `except` statements.
--   [yesqa](https://github.com/asottile/yesqa):
-    remove unneccesary `# noqa` comments, follows additional dependencies listed above.
-    Not included in this template.
--   [autoflake](https://github.com/PyCQA/autoflake):
-    remove unused imports and variables. Not included in this template.
--   [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks.
-    -   **detect-private-key**: checks for the existence of private keys.
-    -   **check-ast**: check whether files parse as valid python.
-    -   **end-of-file-fixer**:check files end in a newline and only a newline.
-    -   **mixed-line-ending**: checks mixed line ending.
-    -   **trailing-whitespace**: trims trailing whitespace.
-    -   **check-case-conflict**: check files that would conflict with case-insensitive file systems.
--   [pyupgrade](https://github.com/asottile/pyupgrade):
-    upgrade syntax for newer versions of the language.
-
-### Notes on pre-commit checks
-
--   **flake8**: to ignore errors, you can add a comment `# noqa` to the offending line.
-    You can also specify the error id to ignore with e.g. `# noqa: E731`.
-    Check [flake8 guide](https://flake8.pycqa.org/en/3.1.1/user/ignoring-errors.html) for reference.
--   You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file.
-    Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` or pre-commit
-    specific config files, such as `.prettierrc.yml` for **prettier** and `.flake8` for **flake8**.