install dev requirements from pyproject.toml

.gitlab-ci.yml

@@ -38,7 +38,7 @@ build-from-prokka-quicktree:
     - install
   script:
     - pip3 install --upgrade pip
-    - pip3 install -r requirements-dev.txt
+    - pip3 install -e .[dev]
     - py.test test/test_install/test_make_prokka-quicktree.py -xv
 
 build-from-prodigal:

make

@@ -86,12 +86,12 @@ def install_all(install_dir, target, dev=False, user=False):
         opt = ""
     if dev:
         logger.info("Installing developer packages needed for PanACoTA")
-        cmd = "pip3 install " + opt + " -e ."
-        cmd2 = "pip3 install -r requirements-dev.txt"
-        error2 = ("Problem while trying to install developer tools. If you have "
-                  "permission errors, try to add 'sudo' before your command line. If "
-                  "you do not have root access, install with the '--user' option")
-        run_cmd(cmd2, error2, eof=True)
+        cmd = "pip3 install " + opt + " -e .[dev]"
+        # cmd2 = "pip3 install -r requirements-dev.txt"
+        # error2 = ("Problem while trying to install developer tools. If you have "
+        #           "permission errors, try to add 'sudo' before your command line. If "
+        #           "you do not have root access, install with the '--user' option")
+        # run_cmd(cmd2, error2, eof=True)
     else:
         cmd = "pip3 install " + opt + " ."
     error = ("A problem occurred while trying to install PanACoTA. If you have "

pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
     "Operating System :: OS Independent",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-dynamic = ["version", "readme", "dependencies"]
+dynamic = ["version", "readme", "dependencies", "optional-dependencies"]
 
 [tool.setuptools.dynamic]
 version = {attr = "PanACoTA.__init__.__version__"}