3.x (#142)

* dbcan 3.x development (#141)

* move cli to the pkg

* add .editorconfig

* add pre-commit-config.yaml

* add .dockerignore

* reformat

* rm setup script and conf

* change ValueError to KeyError

* add readthedocs conf

* add .toml to manage the proj

* add sphinx docs

* .dockerignore

* add user guide doc

* simplify readme

* reorder authors

* :Update 4.1.0: 1. Update dbCAN 2. Harmonizing codes from Jinfang's updates

* fix small bugs

---------

Co-authored-by: HD Yi <haidyi@cs.unc.edu>

.dockerignore

@@ -0,0 +1,5 @@
+.git
+.venv
+.ruff_cache
+db
+docs

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 120
+
+[*.py]
+indent_size = 4
+indent_style = space

.pre-commit-config.yaml

@@ -0,0 +1,57 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/psf/black
+    rev: "23.11.0"
+    hooks:
+      - id: black
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier
+        # Newer versions of node don't work on systems that have an older version of GLIBC
+        # (in particular Ubuntu 18.04 and Centos 7)
+        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+        # https://github.com/jupyterlab/jupyterlab/issues/12675
+        language_version: "17.9.1"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.5
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: check-added-large-files
+      - id: check-toml
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: no-commit-to-branch
+        args: ["--branch=master", "--branch==main"]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc