2025-06-04T22:44:38,345 Created temporary directory: /tmp/pip-build-tracker-yu1sghyi
2025-06-04T22:44:38,348 Initialized build tracking at /tmp/pip-build-tracker-yu1sghyi
2025-06-04T22:44:38,350 Created build tracker: /tmp/pip-build-tracker-yu1sghyi
2025-06-04T22:44:38,351 Entered build tracker: /tmp/pip-build-tracker-yu1sghyi
2025-06-04T22:44:38,352 Created temporary directory: /tmp/pip-wheel-8qi7_22l
2025-06-04T22:44:38,372 Created temporary directory: /tmp/pip-ephem-wheel-cache-0xdafe58
2025-06-04T22:44:38,499 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-04T22:44:38,503 2 location(s) to search for versions of dark-matter:
2025-06-04T22:44:38,503 * https://pypi.org/simple/dark-matter/
2025-06-04T22:44:38,503 * https://www.piwheels.org/simple/dark-matter/
2025-06-04T22:44:38,504 Fetching project page and analyzing links: https://pypi.org/simple/dark-matter/
2025-06-04T22:44:38,505 Getting page https://pypi.org/simple/dark-matter/
2025-06-04T22:44:38,508 Found index url https://pypi.org/simple/
2025-06-04T22:44:38,928 Fetched page https://pypi.org/simple/dark-matter/ as application/vnd.pypi.simple.v1+json
2025-06-04T22:44:39,037   Found link https://files.pythonhosted.org/packages/7a/5d/5704534d2e83673ec3c8534b39fe1a3f071291761d421803f6b2f04ca6b3/dark-matter-1.0.0.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.0
2025-06-04T22:44:39,050   Found link https://files.pythonhosted.org/packages/4a/50/cc5fbbe75b550d6819af04e15ffc633d99b636f2e2d3c22ca4fc09ba2380/dark-matter-1.0.11.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.11
2025-06-04T22:44:39,051   Found link https://files.pythonhosted.org/packages/12/38/d44b5b2e9c08c507a583accb8ee246ce0f98a57c553d06e0199943d0dbf4/dark-matter-1.0.12.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.12
2025-06-04T22:44:39,052   Found link https://files.pythonhosted.org/packages/42/69/f0d13d1e43ec50d1ca85b70c27cc5333f85186668700544a7661c4d6d374/dark-matter-1.0.13.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.13
2025-06-04T22:44:39,054   Found link https://files.pythonhosted.org/packages/30/5a/9c56b0639b13c2c78cad8ac304e9c5d834eed0cab07d0dcd780b7be47249/dark-matter-1.0.16.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.16
2025-06-04T22:44:39,055   Found link https://files.pythonhosted.org/packages/26/8d/eb629def26e051253c4070e70dfc7c8258d513b2685fe4e92bb975b6e613/dark-matter-1.0.19.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.19
2025-06-04T22:44:39,057   Found link https://files.pythonhosted.org/packages/6d/6f/755f4b72e91ce15571d5884761d34627eba8dc173005bc8d41a2e4d2ec81/dark-matter-1.0.27.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.27
2025-06-04T22:44:39,059   Found link https://files.pythonhosted.org/packages/c1/41/a8cb27f9a68dd388473a594c0a5cb162fb1518d16197c357ec3617e9631c/dark-matter-1.0.32.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.32
2025-06-04T22:44:39,061   Found link https://files.pythonhosted.org/packages/26/f5/ea2b1d090cd00bb769d4e07cc4b697373c58dac65a52cf442a4f60a833ba/dark-matter-1.0.34.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.34
2025-06-04T22:44:39,062   Found link https://files.pythonhosted.org/packages/1d/a3/954c4ab15080556dbb33a1c2053ce9028b51cb160099978332b9252b5f93/dark-matter-1.0.36.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.36
2025-06-04T22:44:39,064   Found link https://files.pythonhosted.org/packages/fd/f7/352dcf1f8fb13001175a73acb52fff4bc20760300f87459d7e1e967823a1/dark-matter-1.0.38.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.38
2025-06-04T22:44:39,065   Found link https://files.pythonhosted.org/packages/17/94/5d0c424a52cc3d16793cef2a6b38a8a3542c4bda072c49d61efd18a1ec60/dark-matter-1.0.40.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.40
2025-06-04T22:44:39,067   Found link https://files.pythonhosted.org/packages/4c/d7/9fa11fcb1f9923e3e980f1b493791ca3fbe6920a68a939971fb1eb333d05/dark-matter-1.0.41.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.41
2025-06-04T22:44:39,068   Found link https://files.pythonhosted.org/packages/1b/bb/9a2bffcc74c3bb8c2f45106443174a74dbe3424e45eb483ba7bf72da1fe2/dark-matter-1.0.42.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.42
2025-06-04T22:44:39,070   Found link https://files.pythonhosted.org/packages/e2/dd/cb0a17ce78d39d3b6d6dc93f54c49069b722569042312f7044143a67af30/dark-matter-1.0.43.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.43
2025-06-04T22:44:39,072   Found link https://files.pythonhosted.org/packages/88/ee/c6e7d4142ee1baca46ff0d7f295b7d5a4059648c815de4223f873f17a448/dark-matter-1.0.44.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.44
2025-06-04T22:44:39,073   Found link https://files.pythonhosted.org/packages/7e/71/19001567a982f1ea235095e6f2042990e0666c343bfd985b2c2b8a6a6edc/dark-matter-1.0.45.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.45
2025-06-04T22:44:39,075   Found link https://files.pythonhosted.org/packages/9b/71/0395a4c77fc9443e4b1c8d6d3787d527c2d06ecf56c75db9779bb602d594/dark-matter-1.0.46.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.46
2025-06-04T22:44:39,077   Found link https://files.pythonhosted.org/packages/85/3b/b68351e5280d2f65b26ca3e225a5a0385d921a6d25cef62563eeaec42343/dark-matter-1.0.47.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.47
2025-06-04T22:44:39,078   Found link https://files.pythonhosted.org/packages/fb/4c/6e27c41b817fc86240a956472978b226008da91e8c2b2b5dd991091c3a2d/dark-matter-1.0.48.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.48
2025-06-04T22:44:39,079   Found link https://files.pythonhosted.org/packages/07/65/1253b1fcd6c75fbbc19eee09982ec62023742959583d6687c666befffb71/dark-matter-1.0.49.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.49
2025-06-04T22:44:39,081   Found link https://files.pythonhosted.org/packages/ac/93/e94fa7a2455aa54ebc294bb5bd93c11aca3c461073aee1fab28b4ee380ae/dark-matter-1.0.50.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.50
2025-06-04T22:44:39,082   Found link https://files.pythonhosted.org/packages/b9/ce/7d74daae572ebb32ffdbd439440361f5bf39eb9f9d0f55654878cbd7cbb2/dark-matter-1.0.51.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.51
2025-06-04T22:44:39,083   Found link https://files.pythonhosted.org/packages/cd/fb/8ff473df5992d3cdfc57151ff5595561c42fff343fcc01c76f3b95cd1eb9/dark-matter-1.0.52.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.52
2025-06-04T22:44:39,085   Found link https://files.pythonhosted.org/packages/d4/a7/8e4a7fc079ce3324a605902fb7fe865ab846ba3376408987680cc68703c7/dark-matter-1.0.53.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.53
2025-06-04T22:44:39,086   Found link https://files.pythonhosted.org/packages/a8/50/55d45de9c1903904647e651a955b56dff452d61f9e095a5004a149ab2eca/dark-matter-1.0.54.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.54
2025-06-04T22:44:39,087   Found link https://files.pythonhosted.org/packages/47/41/cc272f599662d184f754abc67ee763ac9da02c5d9ef5d1155effe67d132f/dark-matter-1.0.55.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.55
2025-06-04T22:44:39,089   Found link https://files.pythonhosted.org/packages/d3/d8/250e7506219460c7da81f6f51bf93cce13d21b461392dcbfa1311e504a95/dark-matter-1.0.56.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.56
2025-06-04T22:44:39,090   Found link https://files.pythonhosted.org/packages/81/c7/3bf4ec17c4f0e02ca7741f7ede49d58680f12b48a4a7350031ffe8b38ba1/dark-matter-1.0.57.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.57
2025-06-04T22:44:39,091   Found link https://files.pythonhosted.org/packages/f1/d5/6e02cb418664b484f16ea42b60a86add44acf56dda4875001528957c27b2/dark-matter-1.0.58.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.58
2025-06-04T22:44:39,093   Found link https://files.pythonhosted.org/packages/5a/d3/a69ed2feeac3afcb852a8bcce6cadd5b541cd78de3756f0519a62ca29371/dark-matter-1.0.59.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.59
2025-06-04T22:44:39,094   Found link https://files.pythonhosted.org/packages/68/70/96bd4a89d1c5f40e05d734be94ae1571be35c0b4c4e19e22c0be893c9e1c/dark-matter-1.0.60.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.60
2025-06-04T22:44:39,095   Found link https://files.pythonhosted.org/packages/55/52/ab50ff5d12bb5efd1171a964a4f5baa03edb0091dfa5c79af08fbbe4da16/dark-matter-1.0.61.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.61
2025-06-04T22:44:39,097   Found link https://files.pythonhosted.org/packages/ab/de/cc9a342e642f66e60c8ff98d1786229d5cfcfb0306158f0c19ef61059303/dark-matter-1.0.62.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.62
2025-06-04T22:44:39,098   Found link https://files.pythonhosted.org/packages/cd/a5/713b8a9f25437fafe2a34291ca34f945c9e1394c2e600f73e5abd8e3282e/dark-matter-1.0.63.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.63
2025-06-04T22:44:39,099   Found link https://files.pythonhosted.org/packages/77/fe/320a21e0c4c116bd28487af7156a9937a90dcc44f70c4f720267e9b14291/dark-matter-1.0.64.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.64
2025-06-04T22:44:39,100   Found link https://files.pythonhosted.org/packages/a0/08/9be54a6570a6acf6f87d5ca8ff9f91660697fc32212d0be3601785e796b9/dark-matter-1.0.65.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.65
2025-06-04T22:44:39,102   Found link https://files.pythonhosted.org/packages/7b/61/46caedf674111789641d78a4252b26d1ea43d3d8c77f906b3abc7c638acc/dark-matter-1.0.66.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.66
2025-06-04T22:44:39,103   Found link https://files.pythonhosted.org/packages/97/54/fc8129e31460a4007b2d328e37efeb55a3488b7a7a34592e0c738ac27079/dark-matter-1.0.67.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.67
2025-06-04T22:44:39,104   Found link https://files.pythonhosted.org/packages/e5/33/890848c35cb392c57712943c79ffe317ce401bd2db2a616637719f8c5522/dark-matter-1.0.68.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.68
2025-06-04T22:44:39,106   Found link https://files.pythonhosted.org/packages/c2/23/5e4253583920bada6ee2f5204fbaf8a745527f8ba5c585ac8891fa959991/dark-matter-1.0.69.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.69
2025-06-04T22:44:39,107   Found link https://files.pythonhosted.org/packages/3d/6a/1cf82dcc5f77ac300a3ee4c1fce72edad81280795e42f0da80b67b3a1838/dark-matter-1.0.70.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.70
2025-06-04T22:44:39,109   Found link https://files.pythonhosted.org/packages/64/9a/ace6de00719320e68408c58f3abe036645a29901f17e3e1cd356260cb9f5/dark-matter-1.0.71.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.71
2025-06-04T22:44:39,110   Found link https://files.pythonhosted.org/packages/94/d0/a1e5aabab8ad66683757b3b0569d672da3528a5a8619f830f33c2d6bb179/dark-matter-1.0.72.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.72
2025-06-04T22:44:39,112   Found link https://files.pythonhosted.org/packages/a2/1a/f7d17f7e7d196b1fb5382a27adc6ae61bbc4c47ad812c9e78de890b61743/dark-matter-1.0.73.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.73
2025-06-04T22:44:39,113   Found link https://files.pythonhosted.org/packages/8e/dc/f8fbeb00d964a029f3e444ed65ba9ca0f69e83c4b19d93efb858ac9d67cf/dark-matter-1.0.74.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.74
2025-06-04T22:44:39,115   Found link https://files.pythonhosted.org/packages/26/50/60d51f6d26ec912a10cd058c4221c4794813080bcccd2f5af993a2bfe973/dark-matter-1.0.75.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.75
2025-06-04T22:44:39,116   Found link https://files.pythonhosted.org/packages/03/bb/45b48f894b2b3f2a08e9e3c3c07ce133db94e91a363688f3ab9ce4969d80/dark-matter-1.0.76.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.76
2025-06-04T22:44:39,118   Found link https://files.pythonhosted.org/packages/5a/b2/63dea9b0ab7517190dd58b390cd9f0c007da74ad33c1ce37a74e6640e62c/dark-matter-1.0.77.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.77
2025-06-04T22:44:39,120   Found link https://files.pythonhosted.org/packages/56/a6/ff1dce2b4722ad0fd1dcc5914c1971bcfd1062b1ba50b118503ac201f1d9/dark-matter-1.0.78.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.78
2025-06-04T22:44:39,122   Found link https://files.pythonhosted.org/packages/a6/44/1c0e34e49e6901acc92553a511ac00b2c43efa03d09e290c51f22d1032f2/dark-matter-1.0.79.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.79
2025-06-04T22:44:39,123   Found link https://files.pythonhosted.org/packages/ec/c5/0b771560f096b6ceca2f42c737438d299cbfad32217b7bce5c49408109f2/dark-matter-1.0.80.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.80
2025-06-04T22:44:39,124   Found link https://files.pythonhosted.org/packages/d4/ed/efa93d8e4087caa880c8d66d6ef412eff016bb239ad2402f27159bda3319/dark-matter-1.0.81.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.81
2025-06-04T22:44:39,126   Found link https://files.pythonhosted.org/packages/9a/63/8b9c7378fa5ce52162eef0b86d55106651f7f991bf85081fae3d979e03b8/dark-matter-1.0.82.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.82
2025-06-04T22:44:39,127   Found link https://files.pythonhosted.org/packages/b8/9d/d679c7c2c2117f1a213befba627db8564b541a447e9aded15592c4d88187/dark-matter-1.0.83.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.83
2025-06-04T22:44:39,129   Found link https://files.pythonhosted.org/packages/c2/f4/27b0a93e98fffc72d8e2cefae3d7178d408245390e3165c61424b827ea7a/dark-matter-1.0.84.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.84
2025-06-04T22:44:39,130   Found link https://files.pythonhosted.org/packages/70/74/98991c35e08f4f9faa4c338678d15ecc22c7ada1cec8537a4013661783a7/dark-matter-1.0.85.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.85
2025-06-04T22:44:39,132   Found link https://files.pythonhosted.org/packages/f7/48/a8cb52ec943f30ab2eaa13fcbd13904248dbff48802e044cd13093415b8f/dark-matter-1.0.86.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.86
2025-06-04T22:44:39,134   Found link https://files.pythonhosted.org/packages/60/99/467e7afcc3816958f6b0b65b0b9d5d556901f5cc7505f32723142e23a730/dark-matter-1.0.87.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.87
2025-06-04T22:44:39,135   Found link https://files.pythonhosted.org/packages/96/eb/a304c4774203ca4915a031daf20ef7174fbb6441e5c72900885cee8238ab/dark-matter-1.0.88.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.88
2025-06-04T22:44:39,137   Found link https://files.pythonhosted.org/packages/95/a2/9b1b4b90bcba12dcb6bb46a618f031081b49cedcec407049cd13e0bad838/dark-matter-1.0.89.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.89
2025-06-04T22:44:39,138   Found link https://files.pythonhosted.org/packages/46/9e/932d303fb7765accb20878df3479fcc6f7fa9c3a789143e616d3968e529d/dark-matter-1.0.90.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.90
2025-06-04T22:44:39,140   Found link https://files.pythonhosted.org/packages/a1/8a/757d3cc5c174c076dd4de7b3462997f5686e06784fc7d05bc2d9ecbbed8c/dark-matter-1.0.91.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.91
2025-06-04T22:44:39,141   Found link https://files.pythonhosted.org/packages/34/b2/ba36a28e9d4d398b47609840176e75d245c06ef6f712a8ef2401810c5578/dark-matter-1.0.92.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.92
2025-06-04T22:44:39,142   Found link https://files.pythonhosted.org/packages/4e/be/05871de4f52e365957139663eafee1ea9317bdfa5552c32ebc9fe868d999/dark-matter-1.0.97.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.97
2025-06-04T22:44:39,143   Found link https://files.pythonhosted.org/packages/9a/c2/4637281c6c2cf72c7ae241068d7217b4f4ab239bfa6c859fe95ec32c411b/dark-matter-1.0.98.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.98
2025-06-04T22:44:39,145   Found link https://files.pythonhosted.org/packages/36/2f/6ea29741cda9df28e0e78e9ad5c46532d9c355a8658a33d08e89412d8263/dark-matter-1.0.99.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.99
2025-06-04T22:44:39,146   Found link https://files.pythonhosted.org/packages/bc/09/580b984f227a838207fa95aff9100435482287ae888d5adf7fbfa7b2bb5c/dark-matter-1.0.101.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.101
2025-06-04T22:44:39,147   Found link https://files.pythonhosted.org/packages/89/15/e31a2489ebf0badc0f02778ed22b68e35fe0158076901296f78eb85a2c3c/dark-matter-1.0.106.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.106
2025-06-04T22:44:39,149   Found link https://files.pythonhosted.org/packages/05/fe/3d1303f700e12e04c6b13ac48e42c89213b2519f9dfc3f5dbc13814ad5ea/dark-matter-1.0.107.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.107
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2025-06-04T22:44:39,151   Found link https://files.pythonhosted.org/packages/8c/02/19747c927ee1ff6918de8588d346c5997a1b835d7202d7a445b987fa1b37/dark-matter-1.1.1.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.1.1
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2025-06-04T22:44:39,173   Found link https://files.pythonhosted.org/packages/f0/c4/d1a55a0b5667ba4bffe762916cecd1ef8d5cb71c304b364cd00cc1ddf795/dark-matter-1.1.26.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.1.26
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2025-06-04T22:44:39,179   Found link https://files.pythonhosted.org/packages/b1/4e/b501c50e41f92fe9293d6dae9358073bbfa09666fa1df6afedd9f1523284/dark-matter-1.1.31.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.1.31
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2025-06-04T22:44:39,184   Found link https://files.pythonhosted.org/packages/1c/9e/9e2e8d11ba1ce44d096a3231b8c8ffd532b60badd5cc20af201d32c9d432/dark-matter-2.0.2.tar.gz (from https://pypi.org/simple/dark-matter/), version: 2.0.2
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2025-06-04T22:44:39,187   Found link https://files.pythonhosted.org/packages/94/47/229c1dba2ab7f6d04cb87f11dfecfea88e5d66175d44f0fa127688d70903/dark-matter-2.0.4.tar.gz (from https://pypi.org/simple/dark-matter/), version: 2.0.4
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2025-06-04T22:44:39,195   Found link https://files.pythonhosted.org/packages/88/25/244996f24be2975555f40a0b7a4cdf9656a6d0b207a85d93680f9bd1abbd/dark-matter-3.0.6.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.6
2025-06-04T22:44:39,196   Found link https://files.pythonhosted.org/packages/9f/50/8826b5fb6cfbcf490c7300c9a11767a964369f8a6330702439885fa76e65/dark-matter-3.0.7.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.7
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2025-06-04T22:44:39,199   Found link https://files.pythonhosted.org/packages/84/26/cdbe1fe3689f1828a3eeed326202f69a21b2cdba112d166d0171c2972c4f/dark-matter-3.0.10.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.10
2025-06-04T22:44:39,200   Found link https://files.pythonhosted.org/packages/4f/b8/cd168188be3eb575c92accc2d972f2bd80e487c13bc5119a2cf590d9e6e1/dark-matter-3.0.11.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.11
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2025-06-04T22:44:39,205   Found link https://files.pythonhosted.org/packages/97/dd/c3fe64510486844e98406e7ab66d3fc21dab3e3ce88f6b4d57eb7d80151c/dark-matter-3.0.14.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.14
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2025-06-04T22:44:39,214   Found link https://files.pythonhosted.org/packages/de/be/fd2158dc6a3861332d964fe1a6d9f519b7fe25a0e6083909a6ed9acd5df3/dark-matter-3.0.21.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.21
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2025-06-04T22:44:39,221   Found link https://files.pythonhosted.org/packages/e7/20/3bd386da7171a3150cf8944fa193a36a48cef97476acb04cda73bcc0da98/dark-matter-3.0.28.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.28
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2025-06-04T22:44:39,225   Found link https://files.pythonhosted.org/packages/4e/b2/271c85a7705c934f8a2316d176166ed96160091c80af9fcd22f956b4955f/dark-matter-3.0.31.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.31
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2025-06-04T22:44:39,282   Found link https://files.pythonhosted.org/packages/b3/b4/b660021e23f3d8b70766b3919b8d2e39905da8beacfb92271018d14a1c55/dark-matter-3.0.80.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.0.80
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2025-06-04T22:44:39,370   Found link https://files.pythonhosted.org/packages/62/e7/8217995c8d29d3bbf3fb7044e2a8965cc999699756c172e7c01c6e0fe061/dark-matter-3.1.70.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.1.70
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2025-06-04T22:44:39,382   Found link https://files.pythonhosted.org/packages/bb/91/b9cb62df81f871bb56fb78d6038753845d4d4e90d1737ae6f410160ff31f/dark-matter-3.1.81.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.1.81
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2025-06-04T22:44:39,390   Found link https://files.pythonhosted.org/packages/c0/00/7fae5de4b38e001949cf2f5604456f361a4e4b16dccac360cad9c618774e/dark-matter-3.1.88.tar.gz (from https://pypi.org/simple/dark-matter/), version: 3.1.88
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2025-06-04T22:44:39,412   Found link https://files.pythonhosted.org/packages/62/28/374cc9fa0140ad44b65e22fa41e812098dfd4bcded9d9104179a07c588f3/dark-matter-4.0.16.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.16
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2025-06-04T22:44:39,420   Found link https://files.pythonhosted.org/packages/94/2e/7b6591bebffe84388680e7efad83df91817c286464133f19ec87675c2b4d/dark-matter-4.0.21.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.21
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2025-06-04T22:44:39,432   Found link https://files.pythonhosted.org/packages/b4/3f/61f785a649c7cd6542f16ad9094f99bd4e75fa9847c91b485ca59fe85ec9/dark-matter-4.0.31.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.31
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2025-06-04T22:44:39,469   Found link https://files.pythonhosted.org/packages/c0/ee/097cab71e1df6180f075b63835f4272a3ec2e4ab060650982c57825d4310/dark-matter-4.0.58.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.58
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2025-06-04T22:44:39,479   Found link https://files.pythonhosted.org/packages/96/cc/fe3360ffa2896bf040f07bd2619523fbafd0d9052bac22e83ce4ca910b1c/dark-matter-4.0.66.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.66
2025-06-04T22:44:39,481   Found link https://files.pythonhosted.org/packages/54/5b/1503cd2741ecc6c8d89a12d0cfc669cd84b873cfe9114730c0ecacf099da/dark-matter-4.0.67.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.67
2025-06-04T22:44:39,482   Found link https://files.pythonhosted.org/packages/ba/ec/05375a150b8ca9670354638b4a6f622b6c2807212f9b9a5be9ab02133363/dark-matter-4.0.68.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.68
2025-06-04T22:44:39,483   Found link https://files.pythonhosted.org/packages/8f/d5/4c39e2cfbc6537e67af6724b69f593e2db5f2a6ad38f1af4b5e2300780bb/dark-matter-4.0.69.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.69
2025-06-04T22:44:39,484   Found link https://files.pythonhosted.org/packages/5c/62/83fd2404ae12c888532c48dd97e17b0bdec515b50a071dd680808ecb8354/dark-matter-4.0.70.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.70
2025-06-04T22:44:39,486   Found link https://files.pythonhosted.org/packages/9a/5f/7accc38966e392c0cea694ac1507726f52ae7cbbf4e03454fce3b40d4981/dark-matter-4.0.71.tar.gz (from https://pypi.org/simple/dark-matter/), version: 4.0.71
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2025-06-04T22:44:39,511   Found link https://files.pythonhosted.org/packages/9d/be/019940bef1bc76a002e4074569f5721a3f58509fc3b3a6264b3dcd7e7162/dark-matter-5.0.6.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.6
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2025-06-04T22:44:39,528   Found link https://files.pythonhosted.org/packages/b4/4c/2a8e32660dd2f21795b57489c87e85d724ecec956c2883f819eb289a3768/dark-matter-5.0.22.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.22
2025-06-04T22:44:39,530   Found link https://files.pythonhosted.org/packages/68/b9/bd3cfce28e78b49932e054d2e46efa773a514fdc225522757170d0e50c6e/dark-matter-5.0.23.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.23
2025-06-04T22:44:39,531   Found link https://files.pythonhosted.org/packages/dd/03/9f35f93d305b2ef93b2e7affd934a9a1755600009030988d683cc3e891e5/dark-matter-5.0.24.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.24
2025-06-04T22:44:39,533   Found link https://files.pythonhosted.org/packages/5e/0c/05ab1226f9c7256f51bab667713423abf1cc1d98e7e6b3953c8768322eb1/dark-matter-5.0.25.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.25
2025-06-04T22:44:39,534   Skipping link: No binaries permitted for dark-matter: https://files.pythonhosted.org/packages/11/1e/2ec303be07479099a0d51032ac00680c1c51547f0ebf266705f8c9e50623/dark_matter-5.0.25-py3-none-any.whl (from https://pypi.org/simple/dark-matter/)
2025-06-04T22:44:39,535   Skipping link: No binaries permitted for dark-matter: https://files.pythonhosted.org/packages/df/e1/56c266df121b765097df89259769b777ee0ac2eacc97cbcfa6dda6376f5d/dark_matter-5.0.26-py3-none-any.whl (from https://pypi.org/simple/dark-matter/)
2025-06-04T22:44:39,537   Found link https://files.pythonhosted.org/packages/e7/2f/2fbd7d6ee78f8145c265120540ac9ae4079030ec6c8c9254539d2eb2056a/dark-matter-5.0.27.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.27
2025-06-04T22:44:39,538   Found link https://files.pythonhosted.org/packages/b1/08/2afe385c9945beabaaaaef4bf603ce55ff491d5b6fcc3c616d270073bd8e/dark-matter-5.0.28.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.28
2025-06-04T22:44:39,540   Found link https://files.pythonhosted.org/packages/3b/aa/92b96a5f82d397d6089ef19f96110391cd210ea1c809b354bc2225f5e904/dark-matter-5.0.29.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.29
2025-06-04T22:44:39,541   Found link https://files.pythonhosted.org/packages/42/30/4a5fa39b1f1dbd2fba6d79553aa5535eca6693995fa98d66e811616cb4d4/dark-matter-5.0.30.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.30
2025-06-04T22:44:39,542   Found link https://files.pythonhosted.org/packages/65/a2/6c128a1a6e5d4f637479bc59c847d001fe6563f913f9219b68c338badd14/dark-matter-5.0.31.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.31
2025-06-04T22:44:39,544   Found link https://files.pythonhosted.org/packages/74/d9/d427ce38ee8cac6fc313e23c39364500e28e67f50cdae07b4569d611bf7c/dark-matter-5.0.32.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.32
2025-06-04T22:44:39,545   Found link https://files.pythonhosted.org/packages/f4/d4/43c04d06003563721c453b2d4c6f98a0d5050cc34eeea90df567e8a63b40/dark_matter-5.0.33.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.33
2025-06-04T22:44:39,547   Found link https://files.pythonhosted.org/packages/ab/cc/8243ce21d1654c2d2cfa19e0b46df790ae0aa7c4e5778f7f5112ad697d99/dark_matter-5.0.34.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.34
2025-06-04T22:44:39,549   Found link https://files.pythonhosted.org/packages/53/bc/351a37fdb6bebc765349294462516f822c1e8186229c5dc303470eb1fbab/dark_matter-5.0.36.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.36
2025-06-04T22:44:39,550   Found link https://files.pythonhosted.org/packages/08/e5/13c645ff7936d85e3bdb8b25e3339a0604aed86e9be1c1f90e514d400f60/dark_matter-5.0.37.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.37
2025-06-04T22:44:39,551   Found link https://files.pythonhosted.org/packages/31/83/fcb8eb8e7337146222c16c431287fd7f94261a17a82110fd416976f67d45/dark_matter-5.0.38.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.38
2025-06-04T22:44:39,553   Found link https://files.pythonhosted.org/packages/44/f6/a7409ff4869f6236497c3bfbd69dfe4db1829528a651aaa9b832e636b43c/dark_matter-5.0.39.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.39
2025-06-04T22:44:39,554   Found link https://files.pythonhosted.org/packages/af/89/f46ab96454f6e4140449697c0c7cfdbf8377218be57b6930710768945273/dark_matter-5.0.40.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.40
2025-06-04T22:44:39,556   Found link https://files.pythonhosted.org/packages/3c/cd/6445d6215dce95936b2a43f5b2ff862df2f68a775d0175e5efdd4baee324/dark_matter-5.0.41.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.41
2025-06-04T22:44:39,557   Found link https://files.pythonhosted.org/packages/6c/e8/9f9383cde35b09fc0ca20482bf60c8a02ef4abca7288fc7e512bd7a3f987/dark_matter-5.0.42.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.42
2025-06-04T22:44:39,559   Found link https://files.pythonhosted.org/packages/47/6a/9683937ec02330b1af3823b02865502b1ecdda2c8ade21a18d19450f33c6/dark_matter-5.0.43.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.43
2025-06-04T22:44:39,561 Fetching project page and analyzing links: https://www.piwheels.org/simple/dark-matter/
2025-06-04T22:44:39,562 Getting page https://www.piwheels.org/simple/dark-matter/
2025-06-04T22:44:39,565 Found index url https://www.piwheels.org/simple/
2025-06-04T22:44:39,878 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-04T22:44:40,784 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-04T22:44:42,068 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-04T22:44:44,388 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-04T22:44:48,720 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-04T22:44:49,021 Could not fetch URL https://www.piwheels.org/simple/dark-matter/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/dark-matter/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping
2025-06-04T22:44:49,025 Skipping link: not a file: https://www.piwheels.org/simple/dark-matter/
2025-06-04T22:44:49,027 Skipping link: not a file: https://pypi.org/simple/dark-matter/
2025-06-04T22:44:49,141 Given no hashes to check 1 links for project 'dark-matter': discarding no candidates
2025-06-04T22:44:49,146 Collecting dark-matter==5.0.34
2025-06-04T22:44:49,152   Created temporary directory: /tmp/pip-unpack-4q9wtlv1
2025-06-04T22:44:49,517   Downloading dark_matter-5.0.34.tar.gz (431 kB)
2025-06-04T22:44:50,722   Added dark-matter==5.0.34 from https://files.pythonhosted.org/packages/ab/cc/8243ce21d1654c2d2cfa19e0b46df790ae0aa7c4e5778f7f5112ad697d99/dark_matter-5.0.34.tar.gz to build tracker '/tmp/pip-build-tracker-yu1sghyi'
2025-06-04T22:44:50,727   Running setup.py (path:/tmp/pip-wheel-8qi7_22l/dark-matter_0e20ffa08b924142ae3877eeab9329c1/setup.py) egg_info for package dark-matter
2025-06-04T22:44:50,729   Created temporary directory: /tmp/pip-pip-egg-info-m3v6uevn
2025-06-04T22:44:50,730   Preparing metadata (setup.py): started
2025-06-04T22:44:50,733   Running command python setup.py egg_info
2025-06-04T22:44:52,664   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-04T22:44:52,665   !!

2025-06-04T22:44:52,667           ********************************************************************************
2025-06-04T22:44:52,668           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-04T22:44:52,670           License :: OSI Approved :: MIT License

2025-06-04T22:44:52,673           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-04T22:44:52,674           ********************************************************************************

2025-06-04T22:44:52,676   !!
2025-06-04T22:44:52,677     self._finalize_license_expression()
2025-06-04T22:44:52,745   running egg_info
2025-06-04T22:44:52,840   creating /tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info
2025-06-04T22:44:52,843   writing /tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/PKG-INFO
2025-06-04T22:44:52,850   writing dependency_links to /tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/dependency_links.txt
2025-06-04T22:44:52,855   writing requirements to /tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/requires.txt
2025-06-04T22:44:52,858   writing top-level names to /tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/top_level.txt
2025-06-04T22:44:52,862   writing manifest file '/tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/SOURCES.txt'
2025-06-04T22:44:53,205   reading manifest file '/tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/SOURCES.txt'
2025-06-04T22:44:53,209   adding license file 'LICENSE'
2025-06-04T22:44:53,232   writing manifest file '/tmp/pip-pip-egg-info-m3v6uevn/dark_matter.egg-info/SOURCES.txt'
2025-06-04T22:44:53,491   Preparing metadata (setup.py): finished with status 'done'
2025-06-04T22:44:53,501   Source in /tmp/pip-wheel-8qi7_22l/dark-matter_0e20ffa08b924142ae3877eeab9329c1 has version 5.0.34, which satisfies requirement dark-matter==5.0.34 from https://files.pythonhosted.org/packages/ab/cc/8243ce21d1654c2d2cfa19e0b46df790ae0aa7c4e5778f7f5112ad697d99/dark_matter-5.0.34.tar.gz
2025-06-04T22:44:53,507   Removed dark-matter==5.0.34 from https://files.pythonhosted.org/packages/ab/cc/8243ce21d1654c2d2cfa19e0b46df790ae0aa7c4e5778f7f5112ad697d99/dark_matter-5.0.34.tar.gz from build tracker '/tmp/pip-build-tracker-yu1sghyi'
2025-06-04T22:44:53,549 Created temporary directory: /tmp/pip-unpack-3t32jyk8
2025-06-04T22:44:53,558 Created temporary directory: /tmp/pip-unpack-30malv2l
2025-06-04T22:44:53,560 Building wheels for collected packages: dark-matter
2025-06-04T22:44:53,586   Created temporary directory: /tmp/pip-wheel-06221tcm
2025-06-04T22:44:53,587   DEPRECATION: Building 'dark-matter' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'dark-matter'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-06-04T22:44:53,590   Building wheel for dark-matter (setup.py): started
2025-06-04T22:44:53,593   Destination directory: /tmp/pip-wheel-06221tcm
2025-06-04T22:44:53,595   Running command python setup.py bdist_wheel
2025-06-04T22:44:56,183   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-04T22:44:56,184   !!

2025-06-04T22:44:56,186           ********************************************************************************
2025-06-04T22:44:56,187           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-04T22:44:56,190           License :: OSI Approved :: MIT License

2025-06-04T22:44:56,192           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-04T22:44:56,193           ********************************************************************************

2025-06-04T22:44:56,196   !!
2025-06-04T22:44:56,197     self._finalize_license_expression()
2025-06-04T22:44:56,199   running bdist_wheel
2025-06-04T22:44:56,822   running build
2025-06-04T22:44:56,824   running build_py
2025-06-04T22:44:56,938   creating build/lib/dark
2025-06-04T22:44:56,943   copying dark/simplify.py -> build/lib/dark
2025-06-04T22:44:56,949   copying dark/features.py -> build/lib/dark
2025-06-04T22:44:56,955   copying dark/score.py -> build/lib/dark
2025-06-04T22:44:56,961   copying dark/proteins.py -> build/lib/dark
2025-06-04T22:44:56,967   copying dark/orfs.py -> build/lib/dark
2025-06-04T22:44:56,973   copying dark/database.py -> build/lib/dark
2025-06-04T22:44:56,978   copying dark/errors.py -> build/lib/dark
2025-06-04T22:44:56,984   copying dark/idutils.py -> build/lib/dark
2025-06-04T22:44:56,989   copying dark/windowedIdentity.py -> build/lib/dark
2025-06-04T22:44:56,995   copying dark/taxonomy.py -> build/lib/dark
2025-06-04T22:44:57,002   copying dark/codonDistance.py -> build/lib/dark
2025-06-04T22:44:57,008   copying dark/reads.py -> build/lib/dark
2025-06-04T22:44:57,019   copying dark/distance.py -> build/lib/dark
2025-06-04T22:44:57,023   copying dark/titles.py -> build/lib/dark
2025-06-04T22:44:57,030   copying dark/__init__.py -> build/lib/dark
2025-06-04T22:44:57,035   copying dark/colors.py -> build/lib/dark
2025-06-04T22:44:57,040   copying dark/summarize.py -> build/lib/dark
2025-06-04T22:44:57,046   copying dark/fasta_ss.py -> build/lib/dark
2025-06-04T22:44:57,051   copying dark/aaVars.py -> build/lib/dark
2025-06-04T22:44:57,059   copying dark/consensus.py -> build/lib/dark
2025-06-04T22:44:57,064   copying dark/dimension.py -> build/lib/dark
2025-06-04T22:44:57,068   copying dark/genbank.py -> build/lib/dark
2025-06-04T22:44:57,074   copying dark/sam.py -> build/lib/dark
2025-06-04T22:44:57,082   copying dark/bowtie2.py -> build/lib/dark
2025-06-04T22:44:57,087   copying dark/ncbidb.py -> build/lib/dark
2025-06-04T22:44:57,092   copying dark/sequence.py -> build/lib/dark
2025-06-04T22:44:57,097   copying dark/genomes.py -> build/lib/dark
2025-06-04T22:44:57,103   copying dark/aa.py -> build/lib/dark
2025-06-04T22:44:57,108   copying dark/fastq.py -> build/lib/dark
2025-06-04T22:44:57,112   copying dark/html.py -> build/lib/dark
2025-06-04T22:44:57,117   copying dark/hsp.py -> build/lib/dark
2025-06-04T22:44:57,122   copying dark/btop.py -> build/lib/dark
2025-06-04T22:44:57,128   copying dark/process.py -> build/lib/dark
2025-06-04T22:44:57,133   copying dark/fasta.py -> build/lib/dark
2025-06-04T22:44:57,139   copying dark/entrez.py -> build/lib/dark
2025-06-04T22:44:57,144   copying dark/dna.py -> build/lib/dark
2025-06-04T22:44:57,150   copying dark/mutations.py -> build/lib/dark
2025-06-04T22:44:57,156   copying dark/aligners.py -> build/lib/dark
2025-06-04T22:44:57,161   copying dark/intervals.py -> build/lib/dark
2025-06-04T22:44:57,165   copying dark/alignments.py -> build/lib/dark
2025-06-04T22:44:57,171   copying dark/sqlite3.py -> build/lib/dark
2025-06-04T22:44:57,176   copying dark/ipynb.py -> build/lib/dark
2025-06-04T22:44:57,181   copying dark/trees.py -> build/lib/dark
2025-06-04T22:44:57,186   copying dark/baseimage.py -> build/lib/dark
2025-06-04T22:44:57,190   copying dark/local_align.py -> build/lib/dark
2025-06-04T22:44:57,195   copying dark/cigar.py -> build/lib/dark
2025-06-04T22:44:57,200   copying dark/utils.py -> build/lib/dark
2025-06-04T22:44:57,205   copying dark/filter.py -> build/lib/dark
2025-06-04T22:44:57,212   copying dark/analyze_reads.py -> build/lib/dark
2025-06-04T22:44:57,216   copying dark/progress.py -> build/lib/dark
2025-06-04T22:44:57,221   copying dark/fpcache.py -> build/lib/dark
2025-06-04T22:44:57,225   copying dark/graphics.py -> build/lib/dark
2025-06-04T22:44:57,232   copying dark/consensus-with-debugging.py -> build/lib/dark
2025-06-04T22:44:57,239   creating build/lib/dark/blast
2025-06-04T22:44:57,242   copying dark/blast/score.py -> build/lib/dark/blast
2025-06-04T22:44:57,246   copying dark/blast/hacks.py -> build/lib/dark/blast
2025-06-04T22:44:57,251   copying dark/blast/params.py -> build/lib/dark/blast
2025-06-04T22:44:57,255   copying dark/blast/__init__.py -> build/lib/dark/blast
2025-06-04T22:44:57,259   copying dark/blast/records.py -> build/lib/dark/blast
2025-06-04T22:44:57,263   copying dark/blast/hsp.py -> build/lib/dark/blast
2025-06-04T22:44:57,268   copying dark/blast/alignments.py -> build/lib/dark/blast
2025-06-04T22:44:57,273   copying dark/blast/conversion.py -> build/lib/dark/blast
2025-06-04T22:44:57,280   creating build/lib/dark/diamond
2025-06-04T22:44:57,282   copying dark/diamond/__init__.py -> build/lib/dark/diamond
2025-06-04T22:44:57,286   copying dark/diamond/sam.py -> build/lib/dark/diamond
2025-06-04T22:44:57,291   copying dark/diamond/run.py -> build/lib/dark/diamond
2025-06-04T22:44:57,296   copying dark/diamond/hsp.py -> build/lib/dark/diamond
2025-06-04T22:44:57,301   copying dark/diamond/alignments.py -> build/lib/dark/diamond
2025-06-04T22:44:57,306   copying dark/diamond/conversion.py -> build/lib/dark/diamond
2025-06-04T22:44:57,314   creating build/lib/dark/civ
2025-06-04T22:44:57,317   copying dark/civ/proteins.py -> build/lib/dark/civ
2025-06-04T22:44:57,326   copying dark/civ/__init__.py -> build/lib/dark/civ
2025-06-04T22:44:57,330   copying dark/civ/html.py -> build/lib/dark/civ
2025-06-04T22:44:57,335   copying dark/civ/graphics.py -> build/lib/dark/civ
2025-06-04T22:44:57,351   running build_scripts
2025-06-04T22:44:57,353   creating build/scripts-3.11
2025-06-04T22:44:57,355   copying and adjusting bin/aa-info.py -> build/scripts-3.11
2025-06-04T22:44:57,359   copying and adjusting bin/aa-to-dna.py -> build/scripts-3.11
2025-06-04T22:44:57,363   copying and adjusting bin/aa-to-properties.py -> build/scripts-3.11
2025-06-04T22:44:57,366   copying and adjusting bin/adaptor-distances.py -> build/scripts-3.11
2025-06-04T22:44:57,370   copying and adjusting bin/alignment-panel-civ.py -> build/scripts-3.11
2025-06-04T22:44:57,375   copying and adjusting bin/alignments-per-read.py -> build/scripts-3.11
2025-06-04T22:44:57,378   copying and adjusting bin/bit-score-to-e-value.py -> build/scripts-3.11
2025-06-04T22:44:57,382   copying and adjusting bin/cat-json-blast-records.py -> build/scripts-3.11
2025-06-04T22:44:57,386   copying and adjusting bin/check-fasta-json-blast-consistency.py -> build/scripts-3.11
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2025-06-04T22:44:57,953   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-04T22:44:57,954   !!

2025-06-04T22:44:57,957           ********************************************************************************
2025-06-04T22:44:57,958           Please avoid running ``setup.py`` directly.
2025-06-04T22:44:57,959           Instead, use pypa/build, pypa/installer or other
2025-06-04T22:44:57,961           standards-based tools.

2025-06-04T22:44:57,963           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-04T22:44:57,964           or your builds will no longer be supported.

2025-06-04T22:44:57,966           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-04T22:44:57,967           ********************************************************************************

2025-06-04T22:44:57,970   !!
2025-06-04T22:44:57,972     self.initialize_options()
2025-06-04T22:44:58,042   installing to build/bdist.linux-armv7l/wheel
2025-06-04T22:44:58,044   running install
2025-06-04T22:44:58,076   running install_lib
2025-06-04T22:44:58,170   creating build/bdist.linux-armv7l/wheel
2025-06-04T22:44:58,176   creating build/bdist.linux-armv7l/wheel/dark
2025-06-04T22:44:58,178   copying build/lib/dark/simplify.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,183   copying build/lib/dark/features.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,188   copying build/lib/dark/score.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,192   copying build/lib/dark/proteins.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,199   copying build/lib/dark/orfs.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,202   copying build/lib/dark/database.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,207   copying build/lib/dark/errors.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,211   copying build/lib/dark/idutils.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,215   copying build/lib/dark/windowedIdentity.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,219   copying build/lib/dark/taxonomy.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,224   copying build/lib/dark/codonDistance.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,228   copying build/lib/dark/reads.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,236   copying build/lib/dark/distance.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,240   copying build/lib/dark/titles.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,246   copying build/lib/dark/__init__.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,250   copying build/lib/dark/colors.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,253   copying build/lib/dark/summarize.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,258   copying build/lib/dark/fasta_ss.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,263   copying build/lib/dark/aaVars.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,268   copying build/lib/dark/consensus.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,275   copying build/lib/dark/dimension.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,278   copying build/lib/dark/genbank.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,283   copying build/lib/dark/sam.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,288   copying build/lib/dark/bowtie2.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,293   copying build/lib/dark/ncbidb.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,296   copying build/lib/dark/sequence.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,302   creating build/bdist.linux-armv7l/wheel/dark/diamond
2025-06-04T22:44:58,304   copying build/lib/dark/diamond/__init__.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-04T22:44:58,308   copying build/lib/dark/diamond/sam.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-04T22:44:58,314   copying build/lib/dark/diamond/run.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-04T22:44:58,318   copying build/lib/dark/diamond/hsp.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-04T22:44:58,323   copying build/lib/dark/diamond/alignments.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-04T22:44:58,328   copying build/lib/dark/diamond/conversion.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-04T22:44:58,333   copying build/lib/dark/genomes.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,338   copying build/lib/dark/aa.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,344   copying build/lib/dark/fastq.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,349   copying build/lib/dark/html.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,354   copying build/lib/dark/hsp.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,359   copying build/lib/dark/btop.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,365   creating build/bdist.linux-armv7l/wheel/dark/civ
2025-06-04T22:44:58,368   copying build/lib/dark/civ/proteins.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-04T22:44:58,379   copying build/lib/dark/civ/__init__.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-04T22:44:58,383   copying build/lib/dark/civ/html.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-04T22:44:58,388   copying build/lib/dark/civ/graphics.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-04T22:44:58,395   copying build/lib/dark/process.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,400   copying build/lib/dark/fasta.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,406   copying build/lib/dark/entrez.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,411   copying build/lib/dark/dna.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,416   copying build/lib/dark/mutations.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,421   copying build/lib/dark/aligners.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,427   copying build/lib/dark/intervals.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,432   copying build/lib/dark/alignments.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,439   creating build/bdist.linux-armv7l/wheel/dark/blast
2025-06-04T22:44:58,441   copying build/lib/dark/blast/score.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,446   copying build/lib/dark/blast/hacks.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,451   copying build/lib/dark/blast/params.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,455   copying build/lib/dark/blast/__init__.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,458   copying build/lib/dark/blast/records.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,462   copying build/lib/dark/blast/hsp.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,467   copying build/lib/dark/blast/alignments.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,472   copying build/lib/dark/blast/conversion.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-04T22:44:58,477   copying build/lib/dark/sqlite3.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,482   copying build/lib/dark/ipynb.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,486   copying build/lib/dark/trees.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,491   copying build/lib/dark/baseimage.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,495   copying build/lib/dark/local_align.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,500   copying build/lib/dark/cigar.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,505   copying build/lib/dark/utils.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,511   copying build/lib/dark/filter.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,518   copying build/lib/dark/analyze_reads.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,523   copying build/lib/dark/progress.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,527   copying build/lib/dark/fpcache.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,532   copying build/lib/dark/graphics.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,540   copying build/lib/dark/consensus-with-debugging.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-04T22:44:58,546   running install_egg_info
2025-06-04T22:44:58,633   running egg_info
2025-06-04T22:44:58,712   writing dark_matter.egg-info/PKG-INFO
2025-06-04T22:44:58,719   writing dependency_links to dark_matter.egg-info/dependency_links.txt
2025-06-04T22:44:58,724   writing requirements to dark_matter.egg-info/requires.txt
2025-06-04T22:44:58,726   writing top-level names to dark_matter.egg-info/top_level.txt
2025-06-04T22:44:58,838   reading manifest file 'dark_matter.egg-info/SOURCES.txt'
2025-06-04T22:44:58,863   adding license file 'LICENSE'
2025-06-04T22:44:58,879   writing manifest file 'dark_matter.egg-info/SOURCES.txt'
2025-06-04T22:44:58,903   Copying dark_matter.egg-info to build/bdist.linux-armv7l/wheel/./dark_matter-5.0.34-py3.11.egg-info
2025-06-04T22:44:58,932   running install_scripts
2025-06-04T22:44:58,938   creating build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,941   copying build/scripts-3.11/sam-to-fasta-alignment.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,947   copying build/scripts-3.11/convert-diamond-to-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,952   copying build/scripts-3.11/sam-reference-read-counts.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,956   copying build/scripts-3.11/extract-ORFs.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,962   copying build/scripts-3.11/fastq-set-quality.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,967   copying build/scripts-3.11/write-htcondor-job-spec.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,972   copying build/scripts-3.11/fasta-to-phylip.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,977   copying build/scripts-3.11/dna-to-aa.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,981   copying build/scripts-3.11/split-fasta-by-adaptors.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,986   copying build/scripts-3.11/subset-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,991   copying build/scripts-3.11/dark-matter-version.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:58,996   copying build/scripts-3.11/sff-to-fastq.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,001   copying build/scripts-3.11/alignments-per-read.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,005   copying build/scripts-3.11/fasta-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,010   copying build/scripts-3.11/remove-alrt-from-tree.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,015   copying build/scripts-3.11/filter-fasta-by-complexity.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,020   copying build/scripts-3.11/curate-tree-ete3.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,025   copying build/scripts-3.11/compare-consensuses.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,031   copying build/scripts-3.11/genbank-grep.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,035   copying build/scripts-3.11/make-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,040   copying build/scripts-3.11/run-bwa.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,045   copying build/scripts-3.11/reverse-complement.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,048   copying build/scripts-3.11/convert-sam-to-fastq.sh -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,053   copying build/scripts-3.11/fasta-count.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,058   copying build/scripts-3.11/fasta-sort.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,062   copying build/scripts-3.11/describe-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,066   copying build/scripts-3.11/proteins-to-pathogens.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,071   copying build/scripts-3.11/fasta-translate.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,076   copying build/scripts-3.11/get-features.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,081   copying build/scripts-3.11/codon-distance.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,086   copying build/scripts-3.11/parse-genbank-flat-file.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,090   copying build/scripts-3.11/reference-read-scores-to-JSON.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,094   copying build/scripts-3.11/graph-evalues.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,098   copying build/scripts-3.11/read-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,101   copying build/scripts-3.11/create-newick-relabeling-output.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,105   copying build/scripts-3.11/fasta-subtraction.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,109   copying build/scripts-3.11/ncbi-fetch-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,114   copying build/scripts-3.11/fasta-subset.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,117   copying build/scripts-3.11/fasta-match-offsets.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,121   copying build/scripts-3.11/e-value-to-bit-score.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,125   copying build/scripts-3.11/make-fasta-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,129   copying build/scripts-3.11/get-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,134   copying build/scripts-3.11/aa-to-properties.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,139   copying build/scripts-3.11/aa-to-dna.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,143   copying build/scripts-3.11/fasta-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,147   copying build/scripts-3.11/format-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,151   copying build/scripts-3.11/genome-protein-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,157   copying build/scripts-3.11/aa-info.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,161   copying build/scripts-3.11/check-fasta-json-blast-consistency.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,165   copying build/scripts-3.11/filter-fasta-by-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,169   copying build/scripts-3.11/trim-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,173   copying build/scripts-3.11/bit-score-to-e-value.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,177   copying build/scripts-3.11/ids.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,181   copying build/scripts-3.11/noninteractive-alignment-panel.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,186   copying build/scripts-3.11/get-hosts.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,190   copying build/scripts-3.11/newick-to-ascii.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,194   copying build/scripts-3.11/fasta-find.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,198   copying build/scripts-3.11/fasta-join.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,202   copying build/scripts-3.11/randomize-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,205   copying build/scripts-3.11/fasta-diff.sh -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,209   copying build/scripts-3.11/convert-diamond-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,212   copying build/scripts-3.11/sam-coverage.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,216   copying build/scripts-3.11/get-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
2025-06-04T22:44:59,221   copying build/scripts-3.11/fasta-count-chars.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.34.data/scripts
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2025-06-04T22:44:59,561   creating '/tmp/pip-wheel-06221tcm/dark_matter-5.0.34-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-04T22:44:59,562   adding 'dark/__init__.py'
2025-06-04T22:44:59,563   adding 'dark/aa.py'
2025-06-04T22:44:59,564   adding 'dark/aaVars.py'
2025-06-04T22:44:59,565   adding 'dark/aligners.py'
2025-06-04T22:44:59,566   adding 'dark/alignments.py'
2025-06-04T22:44:59,567   adding 'dark/analyze_reads.py'
2025-06-04T22:44:59,568   adding 'dark/baseimage.py'
2025-06-04T22:44:59,569   adding 'dark/bowtie2.py'
2025-06-04T22:44:59,569   adding 'dark/btop.py'
2025-06-04T22:44:59,570   adding 'dark/cigar.py'
2025-06-04T22:44:59,572   adding 'dark/codonDistance.py'
2025-06-04T22:44:59,575   adding 'dark/colors.py'
2025-06-04T22:44:59,581   adding 'dark/consensus-with-debugging.py'
2025-06-04T22:44:59,587   adding 'dark/consensus.py'
2025-06-04T22:44:59,590   adding 'dark/database.py'
2025-06-04T22:44:59,593   adding 'dark/dimension.py'
2025-06-04T22:44:59,596   adding 'dark/distance.py'
2025-06-04T22:44:59,601   adding 'dark/dna.py'
2025-06-04T22:44:59,604   adding 'dark/entrez.py'
2025-06-04T22:44:59,607   adding 'dark/errors.py'
2025-06-04T22:44:59,611   adding 'dark/fasta.py'
2025-06-04T22:44:59,614   adding 'dark/fasta_ss.py'
2025-06-04T22:44:59,616   adding 'dark/fastq.py'
2025-06-04T22:44:59,619   adding 'dark/features.py'
2025-06-04T22:44:59,623   adding 'dark/filter.py'
2025-06-04T22:44:59,626   adding 'dark/fpcache.py'
2025-06-04T22:44:59,630   adding 'dark/genbank.py'
2025-06-04T22:44:59,633   adding 'dark/genomes.py'
2025-06-04T22:44:59,640   adding 'dark/graphics.py'
2025-06-04T22:44:59,644   adding 'dark/hsp.py'
2025-06-04T22:44:59,648   adding 'dark/html.py'
2025-06-04T22:44:59,650   adding 'dark/idutils.py'
2025-06-04T22:44:59,653   adding 'dark/intervals.py'
2025-06-04T22:44:59,655   adding 'dark/ipynb.py'
2025-06-04T22:44:59,659   adding 'dark/local_align.py'
2025-06-04T22:44:59,663   adding 'dark/mutations.py'
2025-06-04T22:44:59,666   adding 'dark/ncbidb.py'
2025-06-04T22:44:59,669   adding 'dark/orfs.py'
2025-06-04T22:44:59,672   adding 'dark/process.py'
2025-06-04T22:44:59,674   adding 'dark/progress.py'
2025-06-04T22:44:59,681   adding 'dark/proteins.py'
2025-06-04T22:44:59,695   adding 'dark/reads.py'
2025-06-04T22:44:59,706   adding 'dark/sam.py'
2025-06-04T22:44:59,709   adding 'dark/score.py'
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2025-06-04T22:44:59,714   adding 'dark/simplify.py'
2025-06-04T22:44:59,716   adding 'dark/sqlite3.py'
2025-06-04T22:44:59,719   adding 'dark/summarize.py'
2025-06-04T22:44:59,724   adding 'dark/taxonomy.py'
2025-06-04T22:44:59,729   adding 'dark/titles.py'
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2025-06-04T22:44:59,737   adding 'dark/utils.py'
2025-06-04T22:44:59,741   adding 'dark/windowedIdentity.py'
2025-06-04T22:44:59,745   adding 'dark/blast/__init__.py'
2025-06-04T22:44:59,749   adding 'dark/blast/alignments.py'
2025-06-04T22:44:59,754   adding 'dark/blast/conversion.py'
2025-06-04T22:44:59,757   adding 'dark/blast/hacks.py'
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2025-06-04T22:44:59,762   adding 'dark/blast/params.py'
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2025-06-04T22:44:59,768   adding 'dark/blast/score.py'
2025-06-04T22:44:59,772   adding 'dark/civ/__init__.py'
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2025-06-04T22:44:59,794   adding 'dark/civ/proteins.py'
2025-06-04T22:44:59,799   adding 'dark/diamond/__init__.py'
2025-06-04T22:44:59,802   adding 'dark/diamond/alignments.py'
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2025-06-04T22:44:59,813   adding 'dark/diamond/run.py'
2025-06-04T22:44:59,817   adding 'dark/diamond/sam.py'
2025-06-04T22:44:59,824   adding 'dark_matter-5.0.34.data/scripts/aa-info.py'
2025-06-04T22:44:59,827   adding 'dark_matter-5.0.34.data/scripts/aa-to-dna.py'
2025-06-04T22:44:59,830   adding 'dark_matter-5.0.34.data/scripts/aa-to-properties.py'
2025-06-04T22:44:59,832   adding 'dark_matter-5.0.34.data/scripts/adaptor-distances.py'
2025-06-04T22:44:59,843   adding 'dark_matter-5.0.34.data/scripts/alignment-panel-civ.py'
2025-06-04T22:44:59,845   adding 'dark_matter-5.0.34.data/scripts/alignments-per-read.py'
2025-06-04T22:44:59,847   adding 'dark_matter-5.0.34.data/scripts/bit-score-to-e-value.py'
2025-06-04T22:44:59,861   adding 'dark_matter-5.0.34.data/scripts/cat-json-blast-records.py'
2025-06-04T22:44:59,864   adding 'dark_matter-5.0.34.data/scripts/check-fasta-json-blast-consistency.py'
2025-06-04T22:44:59,867   adding 'dark_matter-5.0.34.data/scripts/codon-distance.py'
2025-06-04T22:44:59,870   adding 'dark_matter-5.0.34.data/scripts/compare-consensuses.py'
2025-06-04T22:44:59,874   adding 'dark_matter-5.0.34.data/scripts/compare-sequences.py'
2025-06-04T22:44:59,881   adding 'dark_matter-5.0.34.data/scripts/convert-blast-xml-to-json.py'
2025-06-04T22:44:59,884   adding 'dark_matter-5.0.34.data/scripts/convert-diamond-to-json.py'
2025-06-04T22:44:59,892   adding 'dark_matter-5.0.34.data/scripts/convert-diamond-to-sam.py'
2025-06-04T22:44:59,894   adding 'dark_matter-5.0.34.data/scripts/convert-sam-to-fastq.sh'
2025-06-04T22:44:59,911   adding 'dark_matter-5.0.34.data/scripts/create-newick-relabeling-output.py'
2025-06-04T22:44:59,914   adding 'dark_matter-5.0.34.data/scripts/curate-tree-ete3.py'
2025-06-04T22:44:59,918   adding 'dark_matter-5.0.34.data/scripts/curate-trees.py'
2025-06-04T22:44:59,920   adding 'dark_matter-5.0.34.data/scripts/dark-matter-version.py'
2025-06-04T22:44:59,923   adding 'dark_matter-5.0.34.data/scripts/describe-protein-database.py'
2025-06-04T22:44:59,941   adding 'dark_matter-5.0.34.data/scripts/dna-to-aa.py'
2025-06-04T22:44:59,944   adding 'dark_matter-5.0.34.data/scripts/download-genbank.sh'
2025-06-04T22:44:59,946   adding 'dark_matter-5.0.34.data/scripts/download-refseq-viral-fasta.sh'
2025-06-04T22:44:59,949   adding 'dark_matter-5.0.34.data/scripts/download-refseq-viral-gbff.sh'
2025-06-04T22:44:59,961   adding 'dark_matter-5.0.34.data/scripts/e-value-to-bit-score.py'
2025-06-04T22:44:59,963   adding 'dark_matter-5.0.34.data/scripts/extract-ORFs.py'
2025-06-04T22:44:59,966   adding 'dark_matter-5.0.34.data/scripts/fasta-base-indices.py'
2025-06-04T22:44:59,968   adding 'dark_matter-5.0.34.data/scripts/fasta-count-chars.py'
2025-06-04T22:44:59,981   adding 'dark_matter-5.0.34.data/scripts/fasta-count.py'
2025-06-04T22:44:59,984   adding 'dark_matter-5.0.34.data/scripts/fasta-coverage.py'
2025-06-04T22:44:59,986   adding 'dark_matter-5.0.34.data/scripts/fasta-diff.sh'
2025-06-04T22:44:59,989   adding 'dark_matter-5.0.34.data/scripts/fasta-find.py'
2025-06-04T22:45:00,004   adding 'dark_matter-5.0.34.data/scripts/fasta-identity-table.py'
2025-06-04T22:45:00,006   adding 'dark_matter-5.0.34.data/scripts/fasta-ids.py'
2025-06-04T22:45:00,008   adding 'dark_matter-5.0.34.data/scripts/fasta-join.py'
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2025-06-04T22:45:00,017   adding 'dark_matter-5.0.34.data/scripts/fasta-sort.py'
2025-06-04T22:45:00,019   adding 'dark_matter-5.0.34.data/scripts/fasta-split-by-id.py'
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2025-06-04T22:45:00,024   adding 'dark_matter-5.0.34.data/scripts/fasta-split.py'
2025-06-04T22:45:00,026   adding 'dark_matter-5.0.34.data/scripts/fasta-subset.py'
2025-06-04T22:45:00,028   adding 'dark_matter-5.0.34.data/scripts/fasta-subtraction.py'
2025-06-04T22:45:00,030   adding 'dark_matter-5.0.34.data/scripts/fasta-to-phylip.py'
2025-06-04T22:45:00,033   adding 'dark_matter-5.0.34.data/scripts/fasta-translate.py'
2025-06-04T22:45:00,035   adding 'dark_matter-5.0.34.data/scripts/fasta-variable-sites.py'
2025-06-04T22:45:00,037   adding 'dark_matter-5.0.34.data/scripts/fastq-set-quality.py'
2025-06-04T22:45:00,039   adding 'dark_matter-5.0.34.data/scripts/filter-fasta-by-complexity.py'
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2025-06-04T22:45:00,049   adding 'dark_matter-5.0.34.data/scripts/filter-hits-to-fasta.py'
2025-06-04T22:45:00,054   adding 'dark_matter-5.0.34.data/scripts/filter-reads-alignments.py'
2025-06-04T22:45:00,058   adding 'dark_matter-5.0.34.data/scripts/filter-sam.py'
2025-06-04T22:45:00,062   adding 'dark_matter-5.0.34.data/scripts/format-fasta.py'
2025-06-04T22:45:00,065   adding 'dark_matter-5.0.34.data/scripts/genbank-grep.py'
2025-06-04T22:45:00,070   adding 'dark_matter-5.0.34.data/scripts/genome-protein-summary.py'
2025-06-04T22:45:00,073   adding 'dark_matter-5.0.34.data/scripts/get-features.py'
2025-06-04T22:45:00,076   adding 'dark_matter-5.0.34.data/scripts/get-hosts.py'
2025-06-04T22:45:00,080   adding 'dark_matter-5.0.34.data/scripts/get-reads.py'
2025-06-04T22:45:00,083   adding 'dark_matter-5.0.34.data/scripts/get-taxonomy.py'
2025-06-04T22:45:00,087   adding 'dark_matter-5.0.34.data/scripts/graph-evalues.py'
2025-06-04T22:45:00,090   adding 'dark_matter-5.0.34.data/scripts/ids.py'
2025-06-04T22:45:00,093   adding 'dark_matter-5.0.34.data/scripts/local-align.py'
2025-06-04T22:45:00,097   adding 'dark_matter-5.0.34.data/scripts/make-consensus.py'
2025-06-04T22:45:00,101   adding 'dark_matter-5.0.34.data/scripts/make-fasta-database.py'
2025-06-04T22:45:00,105   adding 'dark_matter-5.0.34.data/scripts/make-protein-database.py'
2025-06-04T22:45:00,108   adding 'dark_matter-5.0.34.data/scripts/ncbi-fetch-id.py'
2025-06-04T22:45:00,111   adding 'dark_matter-5.0.34.data/scripts/newick-to-ascii.py'
2025-06-04T22:45:00,116   adding 'dark_matter-5.0.34.data/scripts/noninteractive-alignment-panel.py'
2025-06-04T22:45:00,120   adding 'dark_matter-5.0.34.data/scripts/parse-genbank-flat-file.py'
2025-06-04T22:45:00,124   adding 'dark_matter-5.0.34.data/scripts/plot-references-by-inter-read-distance.py'
2025-06-04T22:45:00,129   adding 'dark_matter-5.0.34.data/scripts/plot-windowed-identity.py'
2025-06-04T22:45:00,132   adding 'dark_matter-5.0.34.data/scripts/position-summary.py'
2025-06-04T22:45:00,135   adding 'dark_matter-5.0.34.data/scripts/pre-commit.sh'
2025-06-04T22:45:00,138   adding 'dark_matter-5.0.34.data/scripts/print-read-lengths.py'
2025-06-04T22:45:00,142   adding 'dark_matter-5.0.34.data/scripts/proteins-to-pathogens-civ.py'
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2025-06-04T22:45:00,150   adding 'dark_matter-5.0.34.data/scripts/randomize-fasta.py'
2025-06-04T22:45:00,153   adding 'dark_matter-5.0.34.data/scripts/read-blast-json.py'
2025-06-04T22:45:00,157   adding 'dark_matter-5.0.34.data/scripts/read-blast-xml.py'
2025-06-04T22:45:00,160   adding 'dark_matter-5.0.34.data/scripts/reference-read-scores-to-JSON.py'
2025-06-04T22:45:00,163   adding 'dark_matter-5.0.34.data/scripts/relabel-newick-tree.py'
2025-06-04T22:45:00,167   adding 'dark_matter-5.0.34.data/scripts/remove-alrt-from-tree.py'
2025-06-04T22:45:00,170   adding 'dark_matter-5.0.34.data/scripts/reverse-complement.py'
2025-06-04T22:45:00,174   adding 'dark_matter-5.0.34.data/scripts/run-bowtie2.py'
2025-06-04T22:45:00,177   adding 'dark_matter-5.0.34.data/scripts/run-bwa.py'
2025-06-04T22:45:00,183   adding 'dark_matter-5.0.34.data/scripts/sam-coverage-depth.py'
2025-06-04T22:45:00,186   adding 'dark_matter-5.0.34.data/scripts/sam-coverage.py'
2025-06-04T22:45:00,189   adding 'dark_matter-5.0.34.data/scripts/sam-reference-read-counts.py'
2025-06-04T22:45:00,193   adding 'dark_matter-5.0.34.data/scripts/sam-references.py'
2025-06-04T22:45:00,196   adding 'dark_matter-5.0.34.data/scripts/sam-to-fasta-alignment.py'
2025-06-04T22:45:00,199   adding 'dark_matter-5.0.34.data/scripts/sff-to-fastq.py'
2025-06-04T22:45:00,203   adding 'dark_matter-5.0.34.data/scripts/simple-consensus.py'
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2025-06-04T22:45:00,210   adding 'dark_matter-5.0.34.data/scripts/subset-protein-database.py'
2025-06-04T22:45:00,232   adding 'dark_matter-5.0.34.data/scripts/summarize-fasta-bases.py'
2025-06-04T22:45:00,235   adding 'dark_matter-5.0.34.data/scripts/summarize-reads.py'
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2025-06-04T22:45:00,294   adding 'dark_matter-5.0.34.dist-info/licenses/LICENSE'
2025-06-04T22:45:00,296   adding 'dark_matter-5.0.34.dist-info/METADATA'
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2025-06-04T22:45:00,317   removing build/bdist.linux-armv7l/wheel
2025-06-04T22:45:00,654   Building wheel for dark-matter (setup.py): finished with status 'done'
2025-06-04T22:45:00,680   Created wheel for dark-matter: filename=dark_matter-5.0.34-py3-none-any.whl size=404669 sha256=791b0d9a8a3b7c1262394f7548956838d02fa2512e96f85688ccfa8a10051c88
2025-06-04T22:45:00,682   Stored in directory: /tmp/pip-ephem-wheel-cache-0xdafe58/wheels/54/8b/f8/647b047ab8923781ab9476f23e4443eb01d814e630a0f4eed4
2025-06-04T22:45:00,731 Successfully built dark-matter
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