v2.0.5 (#36)

* Bump joblib from 0.17.0 to 1.0.1

Bumps [joblib](https://github.com/joblib/joblib) from 0.17.0 to 1.0.1.
- [Release notes](https://github.com/joblib/joblib/releases)
- [Changelog](https://github.com/joblib/joblib/blob/master/CHANGES.rst)
- [Commits](joblib/joblib@0.17.0...1.0.1)

Signed-off-by: dependabot[bot] <support@github.com>

* Inclued lock file and upgraded dependencies.

* Fixed 1-oligo feature bug.

* Added `ifpd` disclaimer.

* Removed line break

* Bump rich from 9.10.0 to 9.11.0

Bumps [rich](https://github.com/willmcgugan/rich) from 9.10.0 to 9.11.0.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v9.10.0...v9.11.0)

Signed-off-by: dependabot[bot] <support@github.com>

* Bump scipy from 1.6.0 to 1.6.1

Bumps [scipy](https://github.com/scipy/scipy) from 1.6.0 to 1.6.1.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.6.0...v1.6.1)

Signed-off-by: dependabot[bot] <support@github.com>

* Bump rich from 9.11.0 to 9.11.1

Bumps [rich](https://github.com/willmcgugan/rich) from 9.11.0 to 9.11.1.
- [Release notes](https://github.com/willmcgugan/rich/releases)
- [Changelog](https://github.com/willmcgugan/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v9.11.0...v9.11.1)

Signed-off-by: dependabot[bot] <support@github.com>

* Fixed ifpd_serve bug and released.

* Updated lock and fixed queried region passing

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.gitignore

@@ -10,6 +10,3 @@
 
 # pytest cache
 .pytest_cache/*
-
-# Poetry
-poetry.lock

CHANGELOG.md

@@ -10,6 +10,20 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 
+## [2.0.5] - 2021-02-22
+## Added
+- `poetry.lock` file for common dependency versions.
+- Logging commands submitted to queue via `ifpd serve`.
+
+## Changed
+- Upgraded dependencies to latest versions and tested.
+
+## Fixed
+- Minor bug in `ifpd_mkdb` triggered by databases with 1 oligo in a feature. (unlikely scenario)
+- Bug in `ifpd_serve` that added quotes around `--region start end` and caused queries to fail.
+
+
+
 ## [2.0.4] - 2021-02-11
 ### Added
 - Tooltip to GUI explaining that setting `start` and `end` to the same value triggers a query of the whole feature.

README.md

@@ -24,7 +24,7 @@ Once you have `pipx` ready on your system, install the latest stable release of
 
 ## Usage
 
-More details on how to run **iFISH-Probe-Design** are available in the online [documentation](https://ggirelli.github.io/iFISH-probe-design/usage).
+All **iFISH-Probe-Design** commands are accessible via the `ifpd` keyword on the terminal. For each command, you can access its help page by using the `-h` option. More details on how to run `ifpd` are available in the online [documentation](https://ggirelli.github.io/iFISH-probe-design/usage).
 
 ## Contributing
 

ifpd/const.py

@@ -3,6 +3,6 @@
 @contact: gigi.ga90@gmail.com
 """
 
-__version__ = "2.0.4"
+__version__ = "2.0.5"
 
 featureList = ["size", "homogeneity", "centrality"]

ifpd/scripts/mkdb.py

@@ -150,18 +150,20 @@ def sort_oligos(args, chromList):
         if any(startPositions <= endPositions):
             has_overlaps = True
 
+        oligoLengthList = np.unique(chromDF["chromEnd"] - chromDF["chromStart"])
+        oligoLengthRange[0] = min(oligoLengthRange[0], oligoLengthList.min())
+        oligoLengthRange[1] = max(oligoLengthRange[1], oligoLengthList.max())
+
         assert len(startPositions) == len(endPositions)
         if 0 == len(startPositions):
             continue
         oligoMinDist = min(oligoMinDist, min(startPositions - endPositions - 1))
-
-        oligoLengthList = np.unique(chromDF["chromEnd"] - chromDF["chromStart"])
-        oligoLengthRange[0] = min(oligoLengthRange[0], oligoLengthList.min())
-        oligoLengthRange[1] = max(oligoLengthRange[1], oligoLengthList.max())
     return oligoMinDist, oligoLengthRange, has_overlaps
 
 
 def mk_config(args, oligoMinDist, oligoLengthRange, has_overlaps):
+    if np.inf == oligoMinDist:
+        oligoMinDist = 0
     logging.info("Write config file.")
     config = configparser.ConfigParser()
     config["DATABASE"] = {"name": args.dbName, "refGenome": args.refGenome}
@@ -197,6 +199,8 @@ def run(args: argparse.Namespace) -> None:
     logging.info("Parse and write database.")
     chromList = set()
     for line in oligoGenerator:
+        if 0 == len(line.strip()):
+            continue
         line = line.strip().split("\t")
         chrom = line.pop(0)
         line = "\t".join(line) + "\n"

ifpd/sections/probe_design/enquirer.py

@@ -53,13 +53,10 @@ def run(self):
 
                 # If the queue released a task
                 if not type(None) == type(cmd):
-                    logging.info(cmd)
                     outdir_id = self.__get_outdir_id(cmd)
 
                     query_id = os.path.basename(cmd[outdir_id])
-                    logging.info((cmd[outdir_id], query_id))
                     EH = open(f"{cmd[outdir_id]}.error.log", "w+")
-                    logging.info(EH)
 
                     logging.debug(f'Running query "{query_id}"')
                     timestamp = time.time()

ifpd/sections/probe_design/routes.py

@@ -10,6 +10,7 @@
 import ifpd as fp
 from ifpd.sections import routes
 from ifpd.sections.probe_design.query import Query
+import logging
 import os
 import pandas as pd  # type: ignore
 import shlex
@@ -586,9 +587,13 @@ def single_query(routes, self):
         """
 
         formData = bot.request.forms
-        queriedRegion = ""
+        queriedRegion = []
         if formData.start != formData.end:
-            queriedRegion = f"--region {formData.start} {formData.end}"
+            queriedRegion = [
+                "--region",
+                shlex.quote(formData.start),
+                shlex.quote(formData.end),
+            ]
         query_id = "%s:%s:%s:%s" % (
             formData.chromosome,
             formData.start,
@@ -624,7 +629,8 @@ def single_query(routes, self):
             shlex.quote(f"{min_dist}"),
         ]
         if 0 != len(queriedRegion):
-            cmd.extend([shlex.quote(queriedRegion)])
+            cmd.extend(queriedRegion)
+        logging.info(" ".join(cmd))
 
         config = configparser.ConfigParser()
         timestamp = time.time()
@@ -667,9 +673,13 @@ def spotting_query(routes, self):
         """
 
         formData = bot.request.forms
-        queriedRegion = ""
-        if formData.multi_start != formData.multi_end:
-            queriedRegion = f"--region {formData.multi_start} {formData.multi_end}"
+        queriedRegion = []
+        if formData.start != formData.end:
+            queriedRegion = [
+                "--region",
+                shlex.quote(formData.start),
+                shlex.quote(formData.end),
+            ]
         query_id = "%s:%s:%s:%s" % (
             formData.multi_chromosome,
             formData.multi_start,
@@ -706,7 +716,8 @@ def spotting_query(routes, self):
             shlex.quote(f"{formData.multi_win_shift}"),
         ]
         if 0 != len(queriedRegion):
-            cmd.extend([shlex.quote(queriedRegion)])
+            cmd.extend(queriedRegion)
+        logging.info(" ".join(cmd))
 
         config = configparser.ConfigParser()
         timestamp = time.time()