v1.0.1a1

.deepsource.toml

@@ -0,0 +1,16 @@
+version = 1
+
+[[analyzers]]
+name = "shell"
+enabled = true
+
+[[analyzers]]
+name = "secrets"
+enabled = true
+
+[[analyzers]]
+name = "python"
+enabled = true
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"

.github/workflows/pythonpackage.yml

@@ -37,7 +37,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
     runs-on: ${{ matrix.os }}
     steps:
     # Checkout repo and setup python
@@ -62,8 +62,8 @@ jobs:
     - name: Install dependencies
       run: poetry install
       if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-    # run test suite
-    # - name: Test
-    #   run: |
-    #     source .venv/bin/activate
-    #     pytest radiantkit/tests/
+    # run: test suite
+    - name: Test
+      run: |
+        source .venv/bin/activate
+        pytest ifpd2/tests/

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+    python: python3.8
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.0.1"
+    hooks:
+    -   id: check-added-large-files
+    -   id: check-ast
+    -   id: check-docstring-first
+    -   id: check-yaml
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v0.910-1"
+    hooks:
+    -   id: mypy
+-   repo: https://github.com/psf/black
+    rev: "21.9b0"
+    hooks:
+    -   id: black
+-   repo:  https://github.com/PyCQA/flake8
+    rev: "4.0.1"
+    hooks:
+    -   id: flake8
+        args: ["--count", "--select=E9,F63,F7,F82", "--show-source", "--statistics"]
+    -   id: flake8
+        args: ["--count", "--exit-zero", "--max-complexity=5", "--max-line-length=88", "--ignore=E203", "--statistics"]
+-   repo:  https://github.com/jendrikseipp/vulture 
+    rev: "v2.3"
+    hooks:
+    -   id: vulture
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+    -   id: codespell
+        entry: codespell --ignore-words=ignore-spelling-words.txt
+        language: python
+        types: [text]

CHANGELOG.md

@@ -7,9 +7,20 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## Unreleased
-### ...
-- ...
+
+## [1.0.1a1] - 2021-12-07
+### Added
+- New entry points: `db make`, `db dump`, `db info`, `db merge`, and `db_reindex`.
+- Module `io` with parsing functions for output generated via oligo-melting, hush, or OligoArrayAux.
+- Assert for compatibility with a given dtype. (only max value currently checked)
+
+### Changed
+- New database format.
+- `dbchk` entry point changed to `db check`.
+- Dropped sequence length column, as it can be inferred from the end/start columns.
+- Removed `-X` default from `query`.
 
 ## [1.0.0-alpha] - 2021-02-26
 
-[1.0.0-alpha] https://github.com/ggirelli/ifpd/releases/tag/v1.0.0-alpha  
+[1.0.1a1] https://github.com/ggirelli/ifpd2/releases/tag/v1.0.1a1  
+[1.0.0-alpha] https://github.com/ggirelli/ifpd2/releases/tag/v1.0.0-alpha  

README.md

@@ -1,19 +1,19 @@
 # iFISH Probe Design (II)
 
-![](https://img.shields.io/github/license/ggirelli/ifpd2.svg?style=flat)   ![](https://github.com/ggirelli/ifpd2/workflows/Python%20package/badge.svg?branch=main&event=push)  
+[![DOI](https://zenodo.org/badge/210782569.svg)](https://zenodo.org/badge/latestdoi/210782569) ![](https://img.shields.io/github/license/ggirelli/ifpd2.svg?style=flat) ![](https://github.com/ggirelli/ifpd2/workflows/Python%20package/badge.svg?branch=main&event=push)  
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ifpd2) ![PyPI - Format](https://img.shields.io/pypi/format/ifpd2) ![PyPI - Status](https://img.shields.io/pypi/status/ifpd2)  
 ![](https://img.shields.io/github/release/ggirelli/ifpd2.svg?style=flat) ![](https://img.shields.io/github/release-date/ggirelli/ifpd2.svg?style=flat) ![](https://img.shields.io/github/languages/code-size/ggirelli/ifpd2.svg?style=flat)  
 ![](https://img.shields.io/github/watchers/ggirelli/ifpd2.svg?label=Watch&style=social) ![](https://img.shields.io/github/stars/ggirelli/ifpd2.svg?style=social)
 
 [PyPi](https://pypi.org/project/ifpd2/) | [docs](https://ggirelli.github.io/ifpd2/)
 
-`ifpd2` is a Python3.7+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It is based on our previous `ifpd` package, but works with a different and more detailed database format, allowing for more precise control on the probe design process. Read the online [documentation](https://ggirelli.github.io/ifpd2/) for more details.
+`ifpd2` is a Python3.8+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It is based on our previous `ifpd` package, but works with a different and more detailed database format, allowing for more precise control on the probe design process. Read the online [documentation](https://ggirelli.github.io/ifpd2/) for more details.
 
 ## Requirements
 
-`ifpd2` is fully implemented in Python3.7+, thus you need the corresponding Python version to run it. Check out [here](https://realpython.com/installing-python/) how to install Python+ on your machine if you don't have it yet.
+`ifpd2` is fully implemented in Python3.8+, thus you need the corresponding Python version to run it. Check out [here](https://realpython.com/installing-python/) how to install Python+ on your machine if you don't have it yet.
 
-`ifpd2` has been tested with Python 3.7 and 3.8. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/ifpd2#installation)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/ifpd2/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
+`ifpd2` has been tested with Python 3.8 and 3.9. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/ifpd2#installation)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/ifpd2/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
 
 ## Installation
 

ifpd2/__init__.py

@@ -3,17 +3,32 @@
 @contact: gigi.ga90@gmail.com
 """
 
-from ifpd2.const import __version__
-from ifpd2 import asserts
-from ifpd2 import database, walker
+from ifpd2 import asserts, dataclasses, fasta, io
+from ifpd2 import walker, walker2
+from ifpd2 import chromosome, database, region
 from ifpd2 import oligo, probe, probe_set
 
+from importlib.metadata import version, PackageNotFoundError
+from typing import List
+
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    pass
+
 __all__ = [
     "__version__",
     "asserts",
-    "database",
+    "dataclasses",
+    "fasta",
+    "io",
     "walker",
+    "walker2",
+    "chromosome",
+    "database",
+    "region",
     "oligo",
     "probe",
     "probe_set",
 ]
+__path__: List[str]

ifpd2/asserts.py

@@ -4,37 +4,67 @@
 """
 
 import logging
+import numpy as np  # type: ignore
 import sys
 from typing import Callable
 
 
 def ert_type(x, stype, label):
-    assert isinstance(x, stype), f"{label} should be {stype}, {type(x)} instead"
+    if not isinstance(x, stype):
+        raise AssertionError(f"{label} should be {stype}, {type(x)} instead")
 
 
 def ert_multiTypes(x, types, label):
-    cond = any([isinstance(x, t) for t in types])
-    assert cond, f"{label} should be one of {types}, {type(x)} instead"
+    cond = any(isinstance(x, t) for t in types)
+    if not cond:
+        raise AssertionError(f"{label} should be one of {types}, {type(x)} instead")
 
 
 def ert_nonNeg(x, label, include_zero=False):
     if not include_zero:
-        assert x > 0, f"{label} should be greater than 0"
-    else:
-        assert x >= 0, f"{label} should be greater than or equal to 0"
+        if x <= 0:
+            raise AssertionError(f"{label} should be greater than 0")
+    elif x < 0:
+        raise AssertionError(f"{label} should be greater than or equal to 0")
 
 
 def ert_inInterv(x, vmin, vmax, label, leftClose=False, rightClose=True):
     if leftClose:
         if rightClose:
-            assert x >= vmin and x <= vmax, f"expected {vmin}<={label}<={vmax}"
-        else:
-            assert x >= vmin and x < vmax, f"expected {vmin}<={label}<{vmax}"
+            if x < vmin or x > vmax:
+                raise AssertionError(f"expected {vmin}<={label}<={vmax}")
+        elif x < vmin or x >= vmax:
+            raise AssertionError(f"expected {vmin}<={label}<{vmax}")
+    elif rightClose:
+        if x <= vmin or x > vmax:
+            raise AssertionError(f"expected {vmin}<{label}<={vmax}")
+    elif x <= vmin or x >= vmax:
+        raise AssertionError(f"expected {vmin}<{label}<{vmax}")
+
+
+def ert_in_dtype(x, dtype):
+    if dtype.startswith("f"):
+        if x > np.finfo(dtype).max:
+            raise AssertionError(
+                " ".join(
+                    [
+                        "expected to be lower than {dtype} max:",
+                        f"{x} < {np.finfo(dtype).max}",
+                    ]
+                )
+            )
+    elif dtype.startswith("u") or dtype.startswith("i"):
+        if x > np.iinfo(dtype).max:
+            raise AssertionError(
+                " ".join(
+                    [
+                        "expected to be lower than {dtype} max:",
+                        f"{x} < {np.iinfo(dtype).max}",
+                    ]
+                )
+            )
     else:
-        if rightClose:
-            assert x > vmin and x <= vmax, f"expected {vmin}<{label}<={vmax}"
-        else:
-            assert x > vmin and x < vmax, f"expected {vmin}<{label}<{vmax}"
+        logging.warning(f"assert not implemented for dtype '{dtype}'")
 
 
 def enable_rich_assert(fun: Callable) -> Callable:

ifpd2/autocomplete/.ifpd2-complete.bash

@@ -0,0 +1,29 @@
+_ifpd2_completion() {
+    local IFS=$'\n'
+    local response
+
+    response=$(env COMP_WORDS="${COMP_WORDS[*]}" COMP_CWORD=$COMP_CWORD _IFPD2_COMPLETE=bash_complete $1)
+
+    for completion in $response; do
+        IFS=',' read type value <<< "$completion"
+
+        if [[ $type == 'dir' ]]; then
+            COMREPLY=()
+            compopt -o dirnames
+        elif [[ $type == 'file' ]]; then
+            COMREPLY=()
+            compopt -o default
+        elif [[ $type == 'plain' ]]; then
+            COMPREPLY+=($value)
+        fi
+    done
+
+    return 0
+}
+
+_ifpd2_completion_setup() {
+    complete -o nosort -F _ifpd2_completion ifpd2
+}
+
+_ifpd2_completion_setup;
+

ifpd2/autocomplete/.ifpd2-complete.fish

@@ -0,0 +1,22 @@
+function _ifpd2_completion;
+    set -l response;
+
+    for value in (env _IFPD2_COMPLETE=fish_complete COMP_WORDS=(commandline -cp) COMP_CWORD=(commandline -t) ifpd2);
+        set response $response $value;
+    end;
+
+    for completion in $response;
+        set -l metadata (string split "," $completion);
+
+        if test $metadata[1] = "dir";
+            __fish_complete_directories $metadata[2];
+        else if test $metadata[1] = "file";
+            __fish_complete_path $metadata[2];
+        else if test $metadata[1] = "plain";
+            echo $metadata[2];
+        end;
+    end;
+end;
+
+complete --no-files --command ifpd2 --arguments "(_ifpd2_completion)";
+

ifpd2/autocomplete/.ifpd2-complete.zsh

@@ -0,0 +1,35 @@
+#compdef ifpd2
+
+_ifpd2_completion() {
+    local -a completions
+    local -a completions_with_descriptions
+    local -a response
+    (( ! $+commands[ifpd2] )) && return 1
+
+    response=("${(@f)$(env COMP_WORDS="${words[*]}" COMP_CWORD=$((CURRENT-1)) _IFPD2_COMPLETE=zsh_complete ifpd2)}")
+
+    for type key descr in ${response}; do
+        if [[ "$type" == "plain" ]]; then
+            if [[ "$descr" == "_" ]]; then
+                completions+=("$key")
+            else
+                completions_with_descriptions+=("$key":"$descr")
+            fi
+        elif [[ "$type" == "dir" ]]; then
+            _path_files -/
+        elif [[ "$type" == "file" ]]; then
+            _path_files -f
+        fi
+    done
+
+    if [ -n "$completions_with_descriptions" ]; then
+        _describe -V unsorted completions_with_descriptions -U
+    fi
+
+    if [ -n "$completions" ]; then
+        compadd -U -V unsorted -a completions
+    fi
+}
+
+compdef _ifpd2_completion ifpd2;
+