Merge pull request #1 from quadbio/update_paths

Set up mini package

.editorconfig

@@ -0,0 +1,20 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[makefile]
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+indent_style = tab
+indent_size = 4

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: bug
+assignees: ""
+---
+
+<!-- Describe the bug -->
+
+## Description
+
+[TEXT HERE]
+
+<!-- To reproduce -->
+
+```python
+# Your code here
+```
+
+<!-- Put your Error output in this code block (if applicable, else delete the block): -->
+
+<details> <summary> Error output </summary>
+
+```pytb
+# Paste the error output here, if applicable
+```
+
+</details>
+
+## Versions
+
+<details> <summary> Versions </summary>
+
+```pytb
+# Paste the ouput of tradeseq.__version__ and all relevant versions here
+```
+
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: enhancement
+assignees: ""
+---
+
+## Description
+
+**Is your feature request related to a problem? Please describe.**
+
+<!-- A clear and concise description of what the problem is. For example: I need to do [...] which is not possible because [...]. -->
+
+**Describe the solution you are looking for.**
+
+<!-- A clear and concise description of what you want to happen. -->

.github/pull_request_template.md

@@ -0,0 +1,23 @@
+## Changes
+
+<!-- Please remove section if this PR does change an existing feature -->
+
+-   ...
+
+## Bug fixes
+
+<!-- Please give section if this PR does not fix any bugs -->
+
+-   ...
+
+## New
+
+<!-- Please give section if this PR does not implement a new feature -->
+
+-   ...
+
+## Related issues
+
+<!-- Please list related issues. If none exist, open one and reference it here. -->
+
+Closes #

.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+name: Lint
+
+on:
+    push:
+        branches: main
+    pull_request:
+        branches: main
+
+jobs:
+    linting:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v3
+            - name: Setup Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install pre-commit
+            - name: Check pre-commit compatibility
+              run: pre-commit run --all-files --show-diff-on-failure

.gitignore

@@ -157,3 +157,5 @@ figures/
 
 # R stuff
 *.Rhistory
+
+.vscode/*

.pre-commit-config.yaml

@@ -0,0 +1,54 @@
+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: "23.1.0"
+      hooks:
+          - id: black-jupyter
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.4
+      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/charliermarsh/ruff-pre-commit
+      rev: v0.0.253
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      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
+    - 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$'

LICENSE

@@ -25,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,2 +1,3 @@
 # Analysis template repository
-This contains the raw structure I usually use when doing single-cell/spatial data analysis. 
+
+This contains the raw structure I usually use when doing single-cell/spatial data analysis.

analysis/ML-2023-08-09_sample_notebook.ipynb → analysis/ML-2024-04-24_sample_notebook.ipynb

@@ -84,7 +84,7 @@
    "source": [
     "# import standard packages\n",
     "import numpy as np\n",
-    "import pandas as pd \n",
+    "import pandas as pd\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import seaborn as sns\n",

pyproject.toml

@@ -0,0 +1,114 @@
+[build-system]
+requires = ['setuptools', 'setuptools_scm']
+build-backend = 'setuptools.build_meta'
+
+[project]
+name = "fancypackage"
+version = "0.0.0"
+description = "Fancy Package"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Jane Doe"},
+]
+maintainers = [
+    {name = "Jane Doe", email = "[email protected]"},
+]
+urls.Source = "https://github.com/url/to/repo.git"
+urls.Home-page = "https://github.com/url/to/repo.git"
+dependencies = [
+    "anndata",
+    "scanpy",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pre-commit",
+]
+
+[tool.black]
+line-length = 120
+include = '\.pyi?$|\.ipynb?$'
+exclude = '''
+(
+  /(
+      \.eggs
+    | \.git
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | buck-out
+    | build
+    | dist
+  )/
+)
+'''
+
+[tool.isort]
+profile = "black"
+use_parentheses = true
+known_num = "networkx,numpy,pandas,scipy,sklearn,statmodels"
+known_plot = "matplotlib,mplscience,mpl_toolkits,seaborn"
+known_bio = "anndata,scanpy"
+sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,BIO,FIRSTPARTY,LOCALFOLDER"
+no_lines_before = "LOCALFOLDER"
+balanced_wrapping = true
+length_sort = "0"
+indent = "    "
+float_to_top = true
+order_by_type = false
+
+[tool.ruff]
+src = ["."]
+line-length = 119
+target-version = "py38"
+select = [
+    "F",  # Errors detected by Pyflakes
+    "E",  # Error detected by Pycodestyle
+    "W",  # Warning detected by Pycodestyle
+    "D",  # pydocstyle
+    "B",  # flake8-bugbear
+    "TID",  # flake8-tidy-imports
+    "C4",  # flake8-comprehensions
+    "BLE",  # flake8-blind-except
+    "UP",  # pyupgrade
+    "RUF100",  # Report unused noqa directives
+]
+ignore = [
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    "E501",
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    "E731",
+    # allow I, O, l as variable names -> I is the identity matrix
+    "E741",
+    # Missing docstring in public package
+    "D104",
+    # Missing docstring in public module
+    "D100",
+    # Missing docstring in __init__
+    "D107",
+    # Errors from function calls in argument defaults. These are fine when the result is immutable.
+    "B008",
+    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    "D105",
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    "D400",
+    # First line should be in imperative mood; try rephrasing
+    "D401",
+    ## Disable one in each pair of mutually incompatible rules
+    # We don’t want a blank line before a class docstring
+    "D203",
+    # We want docstrings to start immediately after the opening triple quote
+    "D213",
+    # Missing argument description in the docstring TODO: enable
+    "D417",
+    # Unable to detect undefined names
+    "F403",
+    # Underfined, or defined from star imports: module
+    "F405",
+    # Within an except clause, raise exceptions with `raise ... from err`
+    "B904",
+]

src/fancypackage/__init__.py

@@ -0,0 +1,3 @@
+from .core import DATA_DIR, FIG_DIR
+
+__all__ = ["DATA_DIR", "FIG_DIR"]

src/fancypackage/core/__init__.py

@@ -0,0 +1,3 @@
+from ._constants import DATA_DIR, FIG_DIR
+
+__all__ = ["DATA_DIR", "FIG_DIR"]

paths.py → src/fancypackage/core/_constants.py

@@ -1,9 +1,7 @@
 from pathlib import Path
 
-ROOT = Path(__file__).parent.resolve()
+ROOT = Path(__file__).parents[3].resolve()
 
 
 DATA_DIR = ROOT / "data"
 FIG_DIR = ROOT / "figures"
-CODE_DIR = ROOT / "src"
-