Re-automated installation to assure compatibility with auto-building

setup.py

@@ -70,56 +70,28 @@ def run(self):
         # step 1: install DCC, FUCHS and primer design R module
         print("We need to install two other programs of the Dieterich lab circRNA suit, DCC and FUCHS as well "
               "as R package dependencies for other module of circtools")
-        print("We'll install everything for you from GitHub and CRAN for you if you like.")
+        print("We'll install everything for you from GitHub and CRAN for you.")
         print("")
+        print("In order for the circtools primer design module to run, we need to install some R modules.")
+        print("Please make sure R >= 3.4.0 is installed and your R library path is writeable .")
 
-        # answer = query_yes_no("Do you want to continue the automatic dependency installation?\n"
-        #                       "-> \"n\" will only install the circtools base package\n"
-        #                       "-> CTRL-C will abort the installation\n")
-        # if answer:
-        #     subprocess.check_call(["sh", "scripts/external_install.sh"])
-        #
-        #     # step 2: update $PATH
-        #     print("In order for circtools to be globally callable, we would add the installation folder to the $PATH")
-        #     print("variable. Would you like us to do that?")
-        #
-        #     answer = query_yes_no("Update $PATH in .bashrc?")
-        #     if answer:
-        #         print("Running update script...")
-        #         subprocess.check_call(["sh", "scripts/add_to_bashrc.sh"])
-        #     else:
-        #         print("Okay. Please update the $PATH variable yourself, otherwise you may not be able to run circtools.")
-        #     sleep(5)
-        #
-        #     print("")
-        #
-        #     # step 3: create .Renviron file
-        #     print("In order for the circtools primer design module to run, we need to install some R modules.")
-        #     print("Please make sure R >= 3.4.0 is installed.")
-        #     print("Should we update the R package location in order to install package as user?")
-        #
-        #     answer = query_yes_no("Update R_LIB in .Renviron")
-        #     if answer:
-        #         print("Running update script...")
-        #         subprocess.check_call(["sh", "scripts/create_r_environ.sh"])
-        #     else:
-        #         print("Okay. If the R library path is not writeable the installation will most probably fail.")
-        #     sleep(5)
-        #
-        #     print("")
-        #
-        #     # step 4: install OligoArrayAux
-        #     print("The circtools primer module also requires the software \"OligoArrayAux\".")
-        #     print("Should we install the software for you?")
-        #     print("If you choose yes OligoArrayAux will be installed into $HOME/.local/.")
-        #
-        #     answer = query_yes_no("Install OligoArrayAux?")
-        #     if answer:
-        #         print("Running installer script...")
-        #         subprocess.check_call(["sh", "scripts/install_oligo_array_aux.sh"])
-        #     else:
-        #         print("Okay. Please install OligoArrayAux yourself. Otherwise the primer module will not be functional.")
-        #     sleep(5)
+        subprocess.check_call(["sh", "scripts/external_install.sh"])
+        sleep(2)
+        print("")
+
+        # step 2: update $PATH
+        print("In order for circtools to be globally callable, please add the installation folder to the your $PATH"
+              "environment variable")
+        sleep(2)
+
+        print("")
+
+        # step 4: install OligoArrayAux
+        print("The circtools primer module also requires the software \"OligoArrayAux\".")
+        print("Running installer script...")
+        sleep(2)
+
+        subprocess.check_call(["sh", "scripts/install_oligo_array_aux.sh"])
 
         install.run(self)
         # place for post install commands
@@ -183,6 +155,9 @@ def run(self):
         # 'Programming Language :: Python :: 3.2',
         # 'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+
     ],
 
     # What does your project relate to?
@@ -251,4 +226,10 @@ def run(self):
         'develop': PostDevelopCommand,
         'install': PostInstallCommand,
     },
+
+    project_urls={  # Optional
+        'Bug Reports': 'https://github.com/dieterich-lab/circtools/issues',
+        'Dieterich Lab': 'https://dieterichlab.org',
+        'Source': 'https://github.com/dieterich-lab/circtools'
+    },
 )