{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":24,"defaultBranch":"master","name":"bee","ownerLogin":"mariux64","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2015-02-28T13:06:31.000Z","ownerAvatar":"https://github.molgen.mpg.de/avatars/u/7","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1701346540.1812549","currentOid":""},"activityList":{"items":[{"before":"a734919f0cbd58a3bf07fe6b2d537e618064af1f","after":"60a9cceb1f5cbd80acabc867c65b41c420851401","ref":"refs/heads/master","pushedAt":"2023-11-30T12:13:46.677Z","pushType":"push","commitsCount":1,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"Makefile: Update version to 1.2.27","shortMessageHtmlLink":"Makefile: Update version to 1.2.27"}},{"before":"df06443cbbdce9be0127dbf93d65dfb92d2f35dd","after":"a734919f0cbd58a3bf07fe6b2d537e618064af1f","ref":"refs/heads/master","pushedAt":"2023-11-30T12:11:09.364Z","pushType":"pr_merge","commitsCount":3,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"Merge pull request #60 from mariux64/fix-cmake-build\n\nFix cmake build","shortMessageHtmlLink":"Merge pull request #60 from mariux64/fix-cmake-build"}},{"before":null,"after":"5cc3440037f57d0582440ee79d1a18c3ee48375f","ref":"refs/heads/fix-cmake-build","pushedAt":"2023-11-21T12:05:50.711Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"buildtypes: Set default for cmake build type\n\ncmake, by default, uses CMAKE_BULD_TYPE=Debug with implies '-O0'. This\nhas a severe performance impact for most software. Let bee use\nCMAKE_BULD_TYPE=RelWithDebInfo by default, which implies '-O2'.\n\nFor most software, the difference between '-O2' and '-O3' is\nneglectable. Bee packages with special performance considerations, for\nexample zlib, might use -DCMAKE_BUILD_TYPE=Release in their bee file to\nforce '-O3'.","shortMessageHtmlLink":"buildtypes: Set default for cmake build type"}},{"before":"ccc5348c70335502b759c6eb7eb21b8cb3ead2eb","after":"766f24eb2a8da5720c93cc42d72b70c163af9c5a","ref":"refs/heads/fix-symlink-dirs","pushedAt":"2023-10-24T20:31:22.468Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"bee-cache: Use beeindexstr","shortMessageHtmlLink":"bee-cache: Use beeindexstr"}},{"before":null,"after":"ccc5348c70335502b759c6eb7eb21b8cb3ead2eb","ref":"refs/heads/fix-symlink-dirs","pushedAt":"2023-10-24T14:35:13.080Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"Add tool beeindextr\n\nThe bee inventory file `/var/cache/bee/beecache/INVENTORY` contains the\nfilenames of the files installed from bee.\n\nOne problem is, that a file can have more than one name name because of\nsymlinks. For example, we currently have a symlink `/usr/doc ->\nshare/doc` and the inventory currently contains this entry:\n\n cunit-2.1_3-1.x86_64 1619448799 0 0 0100644 683 7eb1686ef4ebac0f4743c407da5aab52 /usr/doc/CUnit/CUnit_doc.css\n\nSo the file is not registerd by its canonical name\n`/usr/share/doc/CUnit/CUnit_doc.css` but by the alias name\n`/usr/doc/CUnit/CUnit_doc.css`. This can happen, if a package is\ninstalled \"through\" a symlink in the system.\n\nThe problem with multiple paths to the same file is, that if one version\nof a package installes a file through one path and another version of a\npackage installs the same file though another path, then the file is\nlost after \"bee update\".\n\nThis is because, all files from the old package, which are not\nregistered by the new version of the same packahe (or any another\ninstalled package) are removed. While the removal works through a\nsymlink, the protection by its single registered ilename does not.\n\nTo mitigate this problem, bee should protect the file itself during\ncertain operations like `bee update`, not just the name variant used in\nthe inventory.\n\nWe want to achive this by translating the directory names used in the\ninventory to their canonical form (if possible).\n\nIn this patch, add a filter tool for the bee index format, which translates\nthe filenames into a canonical form using above caching strategy.\n\nDon't just use realpath(3) or canonicalize_file_name(3) for that,\nbecause this would be much to slow. These functions do readlink() for\nevery path component of the provided name. As we have to do this for\nevery file of the inventory, the system call usage and file system\naccess would explode. Processing the inventory file this way, took more\nthan two minutes.\n\nInstead, cache the results of readlink for a single invocation of the\ntool, so that the operation is done only once per file. Use another\ncache for complete translated path names to reduce the load to the\nreadlink-cache. This way, the same result can be achived in 0.3 seconds.\n\n $ ls -ld /usr/doc\n lrwxrwxrwx 1 root root 9 Mar 7 2011 /usr/doc -> share/doc\n $ grep CUnit_doc.css /var/cache/bee/bee-cache/INVENTORY\n cunit-2.1_3-1.x86_64 1619448799 0 0 0100644 683 7eb1686ef4ebac0f4743c407da5aab52 /usr/doc/CUnit/CUnit_doc.css\n $ ./beeindextr /var/cache/bee/bee-cache/INVENTORY | grep CUnit_doc.css\n cunit-2.1_3-1.x86_64 1619448799 0 0 0100644 683 7eb1686ef4ebac0f4743c407da5aab52 /usr/share/doc/CUnit/CUnit_doc.css","shortMessageHtmlLink":"Add tool beeindextr"}},{"before":"7d4d2bcb3782daded0a71d22450769283b3f2ca5","after":"df06443cbbdce9be0127dbf93d65dfb92d2f35dd","ref":"refs/heads/master","pushedAt":"2023-10-19T08:14:36.601Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"Merge pull request #58 from mariux64/fix-57\n\nbeesh: Abort if download fails","shortMessageHtmlLink":"Merge pull request #58 from mariux64/fix-57"}},{"before":"178e146d52973569644e877eba5243b56884744a","after":"2cc1246b11c6de5c73e0a1761e919e952bc48f04","ref":"refs/heads/fix-57","pushedAt":"2023-10-18T06:22:50.871Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"beesh: Abort if download fails\n\nCurrently, bee doesn't detect the situation when a partial file is\ndownloaded. An incomplete archive usually makes the following extract to\nfail, but the broken file is kept in the cache an needs to be removed\nmanually. Only the the situation, when a failed download produced an\nempty file is explicitly handled.\n\nCurrently, bee contains explicit code to ignore errors from wget. This\ncode existed in the initial commit 067ccf2 (\"initial revision\") from\n2010. The probably reason for it is, that the option `--no-globber` is\nused to avoid downloading a file, which already exists, a second time.\nHowever, wget terminates with a non-zero exit status in that case.\n\nHandle the case of an existing file in the calling code, so that we can\ntreat any wget error as a real error and abort (by the `-e` setting of\nthe shell).\n\nWhile we are at it, change code to download into a tempfile and rename\nit in the success case to avoid problems with partial downloads. This is\nmore robust than the EXIT trap used by current code.","shortMessageHtmlLink":"beesh: Abort if download fails"}},{"before":"21c07bcde6aa1482993cb9b9c8193c1aa79654de","after":"178e146d52973569644e877eba5243b56884744a","ref":"refs/heads/fix-57","pushedAt":"2023-09-11T07:38:24.185Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"beesh: Abort if download fails\n\nCurrently, bee doesn't detect the situation when a partial file is\ndownloaded. An incomplete archive usually makes the following extract to\nfail, but the broken file is kept in the cache an needs to be removed\nmanually. The situation, when a failed download produces an empty file,\nis already handled. Empty cache files are removed when bee is run the\nnext time.\n\nCurrently, bee contains explicit code to ignore errors from wget. This\ncode existed in the initial commit 067ccf2 (\"initial revision\") from\n2010. The reasoning is unclear today and has to be rediscovered if it's\nstill valid. So this patch is kind of experimental and might need\nto be undone.\n\nRemove code to explicitly ignore wget failures. As the script is running\nwith `-e`, a wget failure should invoke the EXIT trap, which removes the\nincomplete file. This is untested.","shortMessageHtmlLink":"beesh: Abort if download fails"}},{"before":null,"after":"21c07bcde6aa1482993cb9b9c8193c1aa79654de","ref":"refs/heads/fix-57","pushedAt":"2023-09-11T07:37:20.415Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"beesh: Abort if download fails\n\nCurrently, bee doesn't detect the situation when a partial file is\ndownloaded. An incomplete archive usually makes the following extract\nfail, but the broken file is kept in the cache an needs to be removed\nmanually. The situation, when a failed download produces an empty file,\nis already handled. Empty cache files are removed when bee is\nrun the next time.\n\nCurrently, bee contains explicit code to ignore errors from wget. This\ncode existed in the initial commit 067ccf2 (\"initial revision\") from\n2010. The reasoning is unclear today and has to be rediscovered if it's\nstill valid. So this patch is kind of experimental and might need to be\nundone.\n\nRemove code to explicitly ignore wget failures. As the script is running\nwith `-e`, a wget failure should invoke the EXIT trap, which removes the\nincomplete file. This is untested.","shortMessageHtmlLink":"beesh: Abort if download fails"}},{"before":"e0c1f0ddc064c38c719a852bd84f601635bb5c8f","after":"7d4d2bcb3782daded0a71d22450769283b3f2ca5","ref":"refs/heads/master","pushedAt":"2023-08-07T17:26:57.124Z","pushType":"push","commitsCount":1,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"Makefile: Update version to 1.2.26","shortMessageHtmlLink":"Makefile: Update version to 1.2.26"}},{"before":"a308312eea7f7f45564dc0a0497534c535909340","after":"e0c1f0ddc064c38c719a852bd84f601635bb5c8f","ref":"refs/heads/master","pushedAt":"2023-05-10T10:54:42.905Z","pushType":"push","commitsCount":1,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"templates/fallback: Remove beezinga.org references\n\nRemove link, because the site no longer is functional.","shortMessageHtmlLink":"templates/fallback: Remove beezinga.org references"}},{"before":"f3a9a54e577e8938823d5cc78a6aa133208bc365","after":"a308312eea7f7f45564dc0a0497534c535909340","ref":"refs/heads/master","pushedAt":"2023-05-10T10:26:40.632Z","pushType":"push","commitsCount":3,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"Merge pull request #56 from mariux64/fix-funny-filenames\n\nFix funny filenames","shortMessageHtmlLink":"Merge pull request #56 from mariux64/fix-funny-filenames"}},{"before":"3eea1112cc0403074400b2d3df962d1c46781c4d","after":"b0915254d181e9e5f403cde06a4029493c6232c6","ref":"refs/heads/fix-funny-filenames","pushedAt":"2023-05-10T10:26:02.088Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"filelist2content: Do not strip whitespace from filenames\n\nSet IFS to the empty string when reading the filenames to avoid leading\nor trailing whitespace to be stripped from the name.\n\nIt's not unlikely that other components of bee fail on filenames with\ntrailing spaces, too, but that is not a reason to keep the bug in this\ntool.","shortMessageHtmlLink":"filelist2content: Do not strip whitespace from filenames"}},{"before":null,"after":"3eea1112cc0403074400b2d3df962d1c46781c4d","ref":"refs/heads/fix-funny-filenames","pushedAt":"2023-05-10T09:32:41.293Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"donald","name":"Donald Buczek","path":"/donald","primaryAvatarUrl":"https://github.molgen.mpg.de/avatars/u/5?s=80"},"commit":{"message":"filelist2content: Do not strip whitespace from filenames\n\nSet IFS to the empty string when reading the filenames to avoid leading\nor trailing whitespace to be stripped from the name.\n\nIt's not unlikely that other compontent of bee fail on filenames with\ntrainling spaces, too, but that is not a reason to keep the bug in this\ntool.","shortMessageHtmlLink":"filelist2content: Do not strip whitespace from filenames"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks4AAkzOAA","startCursor":null,"endCursor":null}},"title":"Activity ยท mariux64/bee"}