{"action":"created","issue":{"url":"https://api.github.com/repos/theislab/scanpy/issues/35","repository_url":"https://api.github.com/repos/theislab/scanpy","labels_url":"https://api.github.com/repos/theislab/scanpy/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/theislab/scanpy/issues/35/comments","events_url":"https://api.github.com/repos/theislab/scanpy/issues/35/events","html_url":"https://github.com/theislab/scanpy/issues/35","id":252337036,"number":35,"title":"psutil error","user":{"login":"hkoohy","id":30291080,"avatar_url":"https://avatars1.githubusercontent.com/u/30291080?v=4","gravatar_id":"","url":"https://api.github.com/users/hkoohy","html_url":"https://github.com/hkoohy","followers_url":"https://api.github.com/users/hkoohy/followers","following_url":"https://api.github.com/users/hkoohy/following{/other_user}","gists_url":"https://api.github.com/users/hkoohy/gists{/gist_id}","starred_url":"https://api.github.com/users/hkoohy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hkoohy/subscriptions","organizations_url":"https://api.github.com/users/hkoohy/orgs","repos_url":"https://api.github.com/users/hkoohy/repos","events_url":"https://api.github.com/users/hkoohy/events{/privacy}","received_events_url":"https://api.github.com/users/hkoohy/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-08-23T16:08:31Z","updated_at":"2017-08-23T21:17:27Z","closed_at":null,"body":"I just have scanpy 0.2.7 and am trying to produce bpmc3 results. BUT right at the beginning (sc.read()) the following error! I will appreciate your help.\r\nthanks\r\n\r\n`--------------------------------------------------------------------------\r\nAttributeError                            Traceback (most recent call last)\r\n<ipython-input-3-ef7315cdb8ff> in <module>()\r\n      2 filename_genes = '/ifs/projects/proj077/backup/public_data/scanpy_tutorials_data/PBMC3K/filtered_gene_bc_matrices/hg19/genes.tsv'\r\n      3 filename_barcodes = '/ifs/projects/proj077/backup/public_data/scanpy_tutorials_data/PBMC3K/filtered_gene_bc_matrices/hg19/barcodes.tsv'\r\n----> 4 adata = sc.read(filename_data, cache=True).transpose()\r\n      5 adata.var_names = np.genfromtxt(filename_genes, dtype=str)[:, 1]\r\n      6 adata.smp_names = np.genfromtxt(filename_barcodes, dtype=str)\r\n\r\n/ifs/devel/hashem/sw-v1/conda/lib/python3.6/site-packages/scanpy/readwrite.py in read(filename_or_filekey, sheet, ext, delimiter, first_column_names, backup_url, return_dict, cache)\r\n     73     if is_filename(filename_or_filekey):\r\n     74         data = read_file(filename_or_filekey, sheet, ext, delimiter,\r\n---> 75                       first_column_names, backup_url, cache)\r\n     76         if isinstance(data, dict):\r\n     77             return data if return_dict else AnnData(data)\r\n\r\n/ifs/devel/hashem/sw-v1/conda/lib/python3.6/site-packages/scanpy/readwrite.py in read_file(filename, sheet, ext, delimiter, first_column_names, backup_url, cache)\r\n    364                 os.makedirs(os.path.dirname(filename_cache))\r\n    365             # write for faster reading when calling the next time\r\n--> 366             write_dict_to_file(filename_cache, ddata, sett.file_format_data)\r\n    367     return ddata\r\n    368 \r\n\r\n/ifs/devel/hashem/sw-v1/conda/lib/python3.6/site-packages/scanpy/readwrite.py in write_dict_to_file(filename, d, ext)\r\n    771             d_write[key] = value\r\n    772     # now open the file\r\n--> 773     wait_until_file_unused(filename)  # thread-safe writing\r\n    774     if ext == 'h5':\r\n    775         with h5py.File(filename, 'w') as f:\r\n\r\n/ifs/devel/hashem/sw-v1/conda/lib/python3.6/site-packages/scanpy/readwrite.py in wait_until_file_unused(filename)\r\n    935 \r\n    936 def wait_until_file_unused(filename):\r\n--> 937     while (filename in get_used_files()):\r\n    938         time.sleep(1)\r\n    939 \r\n\r\n/ifs/devel/hashem/sw-v1/conda/lib/python3.6/site-packages/scanpy/readwrite.py in get_used_files()\r\n    919 def get_used_files():\r\n    920     \"\"\"Get files used by processes with name scanpy.\"\"\"\r\n--> 921     loop_over_scanpy_processes = (proc for proc in psutil.process_iter()\r\n    922                                   if proc.name() == 'scanpy')\r\n    923     filenames = []\r\n\r\nAttributeError: module 'psutil' has no attribute 'process_iter'\r\n\r\n`"},"comment":{"url":"https://api.github.com/repos/theislab/scanpy/issues/comments/324465215","html_url":"https://github.com/theislab/scanpy/issues/35#issuecomment-324465215","issue_url":"https://api.github.com/repos/theislab/scanpy/issues/35","id":324465215,"user":{"login":"falexwolf","id":16916678,"avatar_url":"https://avatars1.githubusercontent.com/u/16916678?v=4","gravatar_id":"","url":"https://api.github.com/users/falexwolf","html_url":"https://github.com/falexwolf","followers_url":"https://api.github.com/users/falexwolf/followers","following_url":"https://api.github.com/users/falexwolf/following{/other_user}","gists_url":"https://api.github.com/users/falexwolf/gists{/gist_id}","starred_url":"https://api.github.com/users/falexwolf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/falexwolf/subscriptions","organizations_url":"https://api.github.com/users/falexwolf/orgs","repos_url":"https://api.github.com/users/falexwolf/repos","events_url":"https://api.github.com/users/falexwolf/events{/privacy}","received_events_url":"https://api.github.com/users/falexwolf/received_events","type":"User","site_admin":false},"created_at":"2017-08-23T21:17:27Z","updated_at":"2017-08-23T21:17:27Z","body":"Does running `pip install psutil --upgrade` help?"}}
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