new: official release

.bumpversion.toml

@@ -0,0 +1,24 @@
+[tool.bumpversion]
+current_version = "1.0.0"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "readme.md"
+
+[[tool.bumpversion.files]]
+filename = "containers/Dockerfile"
+

.devcontainer.json

@@ -0,0 +1,37 @@
+{
+	// setup a container to develop a python package using miniconda3
+	"name": "prevent-nf",
+	"dockerFile": "containers/Dockerfile",
+	"context": ".",
+	"build": {"args": {"CONDA_FILE": "containers/environment.yml"}},
+
+	// Set *default* container specific settings.json values.
+	"settings": {
+
+		"terminal.integrated.profiles.linux": {
+			"bash": {
+				"path": "/bin/bash",
+			}
+		},
+		"terminal.integrated.defaultProfile.windows": "bash",
+		"python.pythonPath": "/opt/conda/bin/python",
+		"python.formatting.provider": "black",
+		"python.formatting.blackPath": "/opt/conda/bin/black",
+		"[python]": {
+			"editor.rulers": [
+				90
+			]
+		},
+	},
+
+	// extensions for vscode
+	"extensions": [
+		"ms-python.python",
+		"stkb.rewrap",
+		"donjayamanne.githistory",
+		"aaron-bond.better-comments",
+		"gruntfuggly.todo-tree",
+		"mhutchie.git-graph"
+	],
+
+}

.gitignore

@@ -0,0 +1,11 @@
+work/
+results/
+logs/
+preprocessing/
+postprocessing/
+foldx-downloads/
+.DS_Store
+*.pyc
+.vscode
+.nextflow*
+optimizing_input.ipynb