{"action":"created","comment":{"url":"https://api.github.com/repos/arfc/saltproc/pulls/comments/212827360","pull_request_review_id":149538882,"id":212827360,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxMjgyNzM2MA==","diff_hunk":"@@ -55,103 +71,280 @@ def __init__(self, steps, cores, nodes, bw, exec_path, restart=False,\n         self.db_file = db_file\n         self.mat_file = mat_file\n         self.current_step = 0\n+        self.init_mat_file = init_mat_file\n+        self.blanket_mat_name = blanket_mat_name\n+        self.driver_mat_name = driver_mat_name\n+        self.driver_vol = driver_vol\n+        self.blanket_vol = blanket_vol\n+        self.get_library_isotopes()\n+        self.prev_qty = 1\n+        self.rep_scheme_init(rep_scheme)\n+        self.two_region = True\n+        if blanket_mat_name == '':\n+            self.two_region = False\n+\n+    def rep_scheme_init(self, rep_scheme):\n+        \"\"\" reprocessing scheme default setting and checking.\n+            1. Undefined parameters set to default value\n+            2. Composition normalized\n+            3. Check input errors for missing elements\n+        \"\"\"\n+        for group, spec in rep_scheme.items():\n+            # set default values:\n+            if 'freq' not in spec.keys():\n+                rep_scheme[group]['freq'] = -1\n+            if 'qty' not in spec.keys():\n+                rep_scheme[group]['qty'] = -1\n+            if 'begin_time' not in spec.keys():\n+                rep_scheme[group]['begin_time'] = -1\n+            if 'end_time' not in spec.keys():\n+                rep_scheme[group]['end_time'] = 1e299\n+            if 'from' not in spec.keys():\n+                rep_scheme[group]['from'] = 'fertile'\n+            if 'to' not in spec.keys():\n+                rep_scheme[group]['to'] = 'waste'\n+            if 'eff' not in spec.keys():\n+                rep_scheme[group]['eff'] = 1\n+\n+            # normalize composition\n+            if 'comp' in spec.keys():\n+                rep_scheme[group]['comp'] = [\n+                    x / sum(rep_scheme[group]['comp']) for x in rep_scheme[group]['comp']]\n+\n+            # check for input errors\n+            if 'element' not in spec.keys():\n+                raise ValueError('Missing elements for %s' % group)\n+            if 'from' not in spec.keys() and 'to' not in spec.keys():\n+                raise ValueError('Missing to AND from for %s' % group)\n+            if spec['from'] == 'fertile' and 'comp' not in spec.keys():\n+                raise ValueError('Must define composition for input material')\n+            if spec['to'] == 'waste':\n+                for el in spec['element']:\n+                    if any(char.isdigit() for char in el):\n+                        raise ValueError('You can only remove Elements')\n+        self.rep_scheme = rep_scheme\n \n     def find_iso_indx(self, keyword):\n-        \"\"\" Returns index number of keword in bumat dictionary\n+        \"\"\" Returns index number of keyword in bumat dictionary\n \n         Parameters:\n         -----------\n         keyword: string or list\n-            keyword to search for - element (e.g. Xe) or isotope (e.g. Pa233)\n+            list for searching element\n+            string for isotope\n \n         Returns:\n         --------\n         numpy array of indices\n         \"\"\"\n-        indx = 0\n         indx_list = []\n+        indx = 0\n         if isinstance(keyword, str):\n-            for key in self.bumat_dict.keys():\n-                if keyword in key:\n-                    indx_list.append(indx)\n-                indx += 1\n+            indx = self.isoname.index(keyword)\n+            indx_list.append(indx)\n         elif isinstance(keyword, list):\n-            for key in self.bumat_dict.keys():\n-                for keywor in keyword:\n-                    if keywor in key:\n+            for key in keyword:\n+                for indx, isotope in enumerate(self.isoname):\n+                    el = \" \".join(re.findall(\"[a-zA-Z]+\", isotope))\n+                    if key == el:\n                         indx_list.append(indx)\n-                indx += 1\n-\n         return np.array(indx_list)\n \n+    def get_library_isotopes(self):\n+        \"\"\" Returns the isotopes in the cross section library\n+\n+        Parameters:\n+        -----------\n+\n+        Returns:\n+        --------\n+        iso_array: array\n+            array of isotopes in cross section library:\n+        \"\"\"\n+        # check if environment variable is set\n+        if os.environ.get('SERPENT_DATA') is not None:\n+            path = os.environ['SERPENT_DATA']\n+        else:\n+            path = ''\n+        with open(self.input_file, 'r') as f:\n+            lines = f.readlines()\n+            for line in lines:\n+                if 'set acelib' in line and '%' != line[0]:\n+                    start = line.index('\"') + 1\n+                    end = line[start:].index('\"') + start\n+                    acelib = line[start:end]\n+        self.lib_isos = []\n+        acelib = path + acelib\n+        with open(acelib, 'r') as f:\n+            lines = f.readlines()\n+            for line in lines:\n+                iso = line.split()[1]\n+                self.lib_isos.append(iso)\n+\n+        self.lib_isos = np.array(self.lib_isos)\n+\n+    def get_mat_def(self):\n+        \"\"\" Get material definition from the initial material definition\n+            file\n+        \"\"\"\n+        with open(self.init_mat_file, 'r') as f:\n+            self.mat_def_dict = OrderedDict({})\n+            lines = f.readlines()\n+            for line in lines:\n+                if 'mat' in line:\n+                    z = line.split()\n+                    key = z[1]\n+                    line = line.split('%')[0]\n+                    self.mat_def_dict[key] = line","path":"saltproc/saltproc.py","position":188,"original_position":188,"commit_id":"ec4b3ca831dd5bb247da63c41196236ad04d78b8","original_commit_id":"ec4b3ca831dd5bb247da63c41196236ad04d78b8","user":{"login":"katyhuff","id":393899,"node_id":"MDQ6VXNlcjM5Mzg5OQ==","avatar_url":"https://avatars2.githubusercontent.com/u/393899?v=4","gravatar_id":"","url":"https://api.github.com/users/katyhuff","html_url":"https://github.com/katyhuff","followers_url":"https://api.github.com/users/katyhuff/followers","following_url":"https://api.github.com/users/katyhuff/following{/other_user}","gists_url":"https://api.github.com/users/katyhuff/gists{/gist_id}","starred_url":"https://api.github.com/users/katyhuff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/katyhuff/subscriptions","organizations_url":"https://api.github.com/users/katyhuff/orgs","repos_url":"https://api.github.com/users/katyhuff/repos","events_url":"https://api.github.com/users/katyhuff/events{/privacy}","received_events_url":"https://api.github.com/users/katyhuff/received_events","type":"User","site_admin":false},"body":"return this object when loop is done.","created_at":"2018-08-26T14:02:58Z","updated_at":"2018-08-26T14:40:20Z","html_url":"https://github.com/arfc/saltproc/pull/29#discussion_r212827360","pull_request_url":"https://api.github.com/repos/arfc/saltproc/pulls/29","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/arfc/saltproc/pulls/comments/212827360"},"html":{"href":"https://github.com/arfc/saltproc/pull/29#discussion_r212827360"},"pull_request":{"href":"https://api.github.com/repos/arfc/saltproc/pulls/29"}}},"pull_request":{"url":"https://api.github.com/repos/arfc/saltproc/pulls/29","id":209295412,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA5Mjk1NDEy","html_url":"https://github.com/arfc/saltproc/pull/29","diff_url":"https://github.com/arfc/saltproc/pull/29.diff","patch_url":"https://github.com/arfc/saltproc/pull/29.patch","issue_url":"https://api.github.com/repos/arfc/saltproc/issues/29","number":29,"state":"open","locked":false,"title":"Saltproc capability addition and UI improvement","user":{"login":"jbae11","id":20345275,"node_id":"MDQ6VXNlcjIwMzQ1Mjc1","avatar_url":"https://avatars1.githubusercontent.com/u/20345275?v=4","gravatar_id":"","url":"https://api.github.com/users/jbae11","html_url":"https://github.com/jbae11","followers_url":"https://api.github.com/users/jbae11/followers","following_url":"https://api.github.com/users/jbae11/following{/other_user}","gists_url":"https://api.github.com/users/jbae11/gists{/gist_id}","starred_url":"https://api.github.com/users/jbae11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbae11/subscriptions","organizations_url":"https://api.github.com/users/jbae11/orgs","repos_url":"https://api.github.com/users/jbae11/repos","events_url":"https://api.github.com/users/jbae11/events{/privacy}","received_events_url":"https://api.github.com/users/jbae11/received_events","type":"User","site_admin":false},"body":"This PR includes addition of the following capabilities:\r\n\r\n1. user-input reprocessing scheme (solves #19)\r\n2. Two-region simulation\r\n3. input file (`run_saltproc.py`) to drive saltproc run (solves #27, #28 )\r\n4. more unit tests\r\n5. 'Smarter' looking up isotopes from the xs library (solves #18)\r\n6. Continuous integration (solves #26)\r\n7. Saving runinfo (user input parameters) into db (solves #24)\r\n8. conversion from .bumat to .dep file (solves #22 )","created_at":"2018-08-18T05:20:30Z","updated_at":"2018-08-26T14:40:20Z","closed_at":null,"merged_at":null,"merge_commit_sha":"dcf92a725fa02bb07b2eb9f0fb07bea6f36285e6","assignee":{"login":"jbae11","id":20345275,"node_id":"MDQ6VXNlcjIwMzQ1Mjc1","avatar_url":"https://avatars1.githubusercontent.com/u/20345275?v=4","gravatar_id":"","url":"https://api.github.com/users/jbae11","html_url":"https://github.com/jbae11","followers_url":"https://api.github.com/users/jbae11/followers","following_url":"https://api.github.com/users/jbae11/following{/other_user}","gists_url":"https://api.github.com/users/jbae11/gists{/gist_id}","starred_url":"https://api.github.com/users/jbae11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbae11/subscriptions","organizations_url":"https://api.github.com/users/jbae11/orgs","repos_url":"https://api.github.com/users/jbae11/repos","events_url":"https://api.github.com/users/jbae11/events{/privacy}","received_events_url":"https://api.github.com/users/jbae11/received_events","type":"User","site_admin":false},"assignees":[{"login":"jbae11","id":20345275,"node_id":"MDQ6VXNlcjIwMzQ1Mjc1","avatar_url":"https://avatars1.githubusercontent.com/u/20345275?v=4","gravatar_id":"","url":"https://api.github.com/users/jbae11","html_url":"https://github.com/jbae11","followers_url":"https://api.github.com/users/jbae11/followers","following_url":"https://api.github.com/users/jbae11/following{/other_user}","gists_url":"https://api.github.com/users/jbae11/gists{/gist_id}","starred_url":"https://api.github.com/users/jbae11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbae11/subscriptions","organizations_url":"https://api.github.com/users/jbae11/orgs","repos_url":"https://api.github.com/users/jbae11/repos","events_url":"https://api.github.com/users/jbae11/events{/privacy}","received_events_url":"https://api.github.com/users/jbae11/received_events","type":"User","site_admin":false}],"requested_reviewers":[{"login":"andrewryh","id":20629016,"node_id":"MDQ6VXNlcjIwNjI5MDE2","avatar_url":"https://avatars0.githubusercontent.com/u/20629016?v=4","gravatar_id":"","url":"https://api.github.com/users/andrewryh","html_url":"https://github.com/andrewryh","followers_url":"https://api.github.com/users/andrewryh/followers","following_url":"https://api.github.com/users/andrewryh/following{/other_user}","gists_url":"https://api.github.com/users/andrewryh/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewryh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewryh/subscriptions","organizations_url":"https://api.github.com/users/andrewryh/orgs","repos_url":"https://api.github.com/users/andrewryh/repos","events_url":"https://api.github.com/users/andrewryh/events{/privacy}","received_events_url":"https://api.github.com/users/andrewryh/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[{"id":709562065,"node_id":"MDU6TGFiZWw3MDk1NjIwNjU=","url":"https://api.github.com/repos/arfc/saltproc/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"milestone":null,"commits_url":"https://api.github.com/repos/arfc/saltproc/pulls/29/commits","review_comments_url":"https://api.github.com/repos/arfc/saltproc/pulls/29/comments","review_comment_url":"https://api.github.com/repos/arfc/saltproc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/arfc/saltproc/issues/29/comments","statuses_url":"https://api.github.com/repos/arfc/saltproc/statuses/ec4b3ca831dd5bb247da63c41196236ad04d78b8","head":{"label":"jbae11:combined","ref":"combined","sha":"ec4b3ca831dd5bb247da63c41196236ad04d78b8","user":{"login":"jbae11","id":20345275,"node_id":"MDQ6VXNlcjIwMzQ1Mjc1","avatar_url":"https://avatars1.githubusercontent.com/u/20345275?v=4","gravatar_id":"","url":"https://api.github.com/users/jbae11","html_url":"https://github.com/jbae11","followers_url":"https://api.github.com/users/jbae11/followers","following_url":"https://api.github.com/users/jbae11/following{/other_user}","gists_url":"https://api.github.com/users/jbae11/gists{/gist_id}","starred_url":"https://api.github.com/users/jbae11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbae11/subscriptions","organizations_url":"https://api.github.com/users/jbae11/orgs","repos_url":"https://api.github.com/users/jbae11/repos","events_url":"https://api.github.com/users/jbae11/events{/privacy}","received_events_url":"https://api.github.com/users/jbae11/received_events","type":"User","site_admin":false},"repo":{"id":122673824,"node_id":"MDEwOlJlcG9zaXRvcnkxMjI2NzM4MjQ=","name":"saltproc","full_name":"jbae11/saltproc","owner":{"login":"jbae11","id":20345275,"node_id":"MDQ6VXNlcjIwMzQ1Mjc1","avatar_url":"https://avatars1.githubusercontent.com/u/20345275?v=4","gravatar_id":"","url":"https://api.github.com/users/jbae11","html_url":"https://github.com/jbae11","followers_url":"https://api.github.com/users/jbae11/followers","followin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