## Change Log ### v3.0.dev4019 (2021/06/25 16:09 +00:00) - [#1664](https://github.com/tardis-sn/tardis/pull/1664) Use conda-forge packages instead of pypi (#1664) (@epassaro) - [#1667](https://github.com/tardis-sn/tardis/pull/1667) Moving Profiling Page (#1667) (@smithis7) - [#1659](https://github.com/tardis-sn/tardis/pull/1659) Restructure Documentation pt. 2 (#1659) (@smithis7) - [#1656](https://github.com/tardis-sn/tardis/pull/1656) Editing sponsors and credits pages of documentation (#1656) (@smithis7) - [#1597](https://github.com/tardis-sn/tardis/pull/1597) Added value error to ensure active virtual packet logging in SDECPlotter (#1597) (@yuyizheng1112) - [#1630](https://github.com/tardis-sn/tardis/pull/1630) Fix FileExistsError in to_hdf() (#1630) (@yuyizheng1112) - [#1641](https://github.com/tardis-sn/tardis/pull/1641) Editing Installation Page (#1641) (@musabbihaz) - [#1657](https://github.com/tardis-sn/tardis/pull/1657) Add SnakeViz profiling example (#1657) (@KevinCawley) ### v3.0.dev4010 (2021/06/18 21:22 +00:00) - [#1644](https://github.com/tardis-sn/tardis/pull/1644) add mailmap check workflow (#1644) (@epassaro) - [#1589](https://github.com/tardis-sn/tardis/pull/1589) Adding Interactive Initialization Documentation (#1589) (@smithis7) - [#1627](https://github.com/tardis-sn/tardis/pull/1627) Correct misspelling in sdec_plot (#1627) (@yuyizheng1112) - [#1632](https://github.com/tardis-sn/tardis/pull/1632) Formatting Logging Output for Simulation (#1632) (@DhruvSondhi) - [#1652](https://github.com/tardis-sn/tardis/pull/1652) Changes to tardis environment (#1652) (@epassaro) - [#1650](https://github.com/tardis-sn/tardis/pull/1650) Added functionality to detect running environment for simulations (#1650) (@DhruvSondhi) - [#1615](https://github.com/tardis-sn/tardis/pull/1615) Added flag to disable notebook rendering in Sphinx (#1615) (@epassaro) - [#1651](https://github.com/tardis-sn/tardis/pull/1651) force orphan gh-pages branch (#1651) (@epassaro) - [#1643](https://github.com/tardis-sn/tardis/pull/1643) Restructure Documentation (#1643) (@smithis7) - [#1647](https://github.com/tardis-sn/tardis/pull/1647) Added fix for the packet logging while parallelism is enbaled. The vpacket collections are cached at the start of the loop and data is extracted afterwards (#1647) (@Rodot-) - [#1645](https://github.com/tardis-sn/tardis/pull/1645) Configured codecov (#1645) (@epassaro) - [#1586](https://github.com/tardis-sn/tardis/pull/1586) Added GitHub pages instructions (#1586) (@epassaro) ### v3.0.dev3998 (2021/06/14 14:52 +00:00) - [#1648](https://github.com/tardis-sn/tardis/pull/1648) Fixed compareWith parameter in release pipeline (#1648) (@epassaro) - [#1609](https://github.com/tardis-sn/tardis/pull/1609) update refdata procedure docs (#1609) (@epassaro) - [#1635](https://github.com/tardis-sn/tardis/pull/1635) Run tests before making a new release (#1635) (@epassaro) - [#1617](https://github.com/tardis-sn/tardis/pull/1617) Fixing docstrings & indentation related warnings for Sphinx (#1617) (@DhruvSondhi) - [#1565](https://github.com/tardis-sn/tardis/pull/1565) Fix for close line test. (#1565) (@Rodot-) - [#1639](https://github.com/tardis-sn/tardis/pull/1639) push montecarlo data (#1639) (@epassaro) - [#1595](https://github.com/tardis-sn/tardis/pull/1595) move zenodo pipeline to GA (#1595) (@epassaro) - [#1623](https://github.com/tardis-sn/tardis/pull/1623) force pyne nomoab_openmc version (#1623) (@epassaro) - [#1622](https://github.com/tardis-sn/tardis/pull/1622) Adding GitHub to sponsors page (#1622) (@smithis7) - [#1631](https://github.com/tardis-sn/tardis/pull/1631) update mailmap and orcid (#1631) (@epassaro) - [#1619](https://github.com/tardis-sn/tardis/pull/1619) disable repeat on pr comment (#1619) (@epassaro) ### v3.0.dev3983 (2021/06/04 16:50 +00:00) - [#1555](https://github.com/tardis-sn/tardis/pull/1555) Replacing the contents of the news section with TARDIS twitter feed (#1555) (@atharva-2001) - [#1610](https://github.com/tardis-sn/tardis/pull/1610) add token at checkout step (#1610) (@epassaro) - [#1594](https://github.com/tardis-sn/tardis/pull/1594) Fixing JSON Schema not Rendering Properly in the Documentation (#1594) (@DhruvSondhi) - [#1607](https://github.com/tardis-sn/tardis/pull/1607) SDEC Visibility Fix (#1607) (@atharva-2001) - [#1603](https://github.com/tardis-sn/tardis/pull/1603) change bot email (#1603) (@epassaro) - [#1601](https://github.com/tardis-sn/tardis/pull/1601) fixing doc build (#1601) (@smithis7) - [#1602](https://github.com/tardis-sn/tardis/pull/1602) add fetch depth param to changelog workflow (#1602) (@epassaro) - [#1588](https://github.com/tardis-sn/tardis/pull/1588) Added PR review checklist workflow (#1588) (@aribalam) - [#1592](https://github.com/tardis-sn/tardis/pull/1592) Flexible packet initial radius (#1592) (@andrewfullard) - [#1598](https://github.com/tardis-sn/tardis/pull/1598) Resolving warnings in ADS notebook (#1598) (@smithis7) - [#1596](https://github.com/tardis-sn/tardis/pull/1596) Fixing bibliography in documentation build (#1596) (@smithis7) - [#1590](https://github.com/tardis-sn/tardis/pull/1590) Fixing inconsistencies for `rst` formatting in Docs (Second Iteration) (#1590) (@DhruvSondhi) ### v3.0.dev3970 (2021/05/28 21:43 +00:00) - [#1570](https://github.com/tardis-sn/tardis/pull/1570) add fetch depth param to Azure template (#1570) (@epassaro) - [#1567](https://github.com/tardis-sn/tardis/pull/1567) review environment file (#1567) (@epassaro) - [#1584](https://github.com/tardis-sn/tardis/pull/1584) Making sponsors page of documentation (#1584) (@smithis7) - [#1577](https://github.com/tardis-sn/tardis/pull/1577) Fixing issues with `Citations` & `Label` references in Docs (@DhruvSondhi) - [#1581](https://github.com/tardis-sn/tardis/pull/1581) changes to badges (@epassaro) ### v3.0.dev3959 (2021/05/21 18:44 +00:00) - [#1582](https://github.com/tardis-sn/tardis/pull/1582) Fixing `Team` Link redirection in Code Of Conduct (@DhruvSondhi) ### v3.0.dev3957 (2021/05/20 19:27 +00:00) - [#1571](https://github.com/tardis-sn/tardis/pull/1571) Fix numba deprecation (#1571) (@KevinCawley) - [#1578](https://github.com/tardis-sn/tardis/pull/1578) minor changes to compare refdata pipeline (#1578) (@epassaro) - [#1557](https://github.com/tardis-sn/tardis/pull/1557) Changed Quickstart Example according to #1477 (#1557) (@aribalam) - [#1575](https://github.com/tardis-sn/tardis/pull/1575) Fixing virtual_packet_logging instructions for line info widget (#1575) (@DhruvSondhi) - [#1551](https://github.com/tardis-sn/tardis/pull/1551) Revert "Adding Instructions for enabling virtual_packet_logging (#1551)" (#1574) (@jaladh-singhal) ### v3.0.dev3952 (2021/05/14 17:44 +00:00) - [#1559](https://github.com/tardis-sn/tardis/pull/1559) Added support for passing Configuration object in run_tardis (#1559) (@aribalam) - [#1553](https://github.com/tardis-sn/tardis/pull/1553) Fixing Config Validator rst formatting (#1553) (@DhruvSondhi) - [#1551](https://github.com/tardis-sn/tardis/pull/1551) Adding Instructions for enabling virtual_packet_logging (#1551) (@DhruvSondhi) - [#1528](https://github.com/tardis-sn/tardis/pull/1528) Revising "Packet Propagation" page of physics docs (#1528) (@smithis7) - [#1569](https://github.com/tardis-sn/tardis/pull/1569) [build docs] fixing build problem (#1569) (@smithis7) ### v3.0.dev3947 (2021/05/12 20:42 +00:00) - [#1566](https://github.com/tardis-sn/tardis/pull/1566) better handling of pickle5 backport (#1566) (@epassaro) - [#1562](https://github.com/tardis-sn/tardis/pull/1562) added symlinks for tardis_example.yml (#1562) (@parikshit14) ### v3.0.dev3945 (2021/05/05 14:03 +00:00) - [#1434](https://github.com/tardis-sn/tardis/pull/1434) create update refdata pipeline (#1434) (@epassaro) - [#1554](https://github.com/tardis-sn/tardis/pull/1554) Adding Config Value Validation for Different Parameters via Config File (#1554) (@DhruvSondhi) - [#1549](https://github.com/tardis-sn/tardis/pull/1549) Numba formal integral (#1549) (@Rodot-) - [#1546](https://github.com/tardis-sn/tardis/pull/1546) resolves issue #1370 bad YAML Output (#1546) (@atharva-2001) - [#1543](https://github.com/tardis-sn/tardis/pull/1543) Restructuring r_packet.py (#1543) (@andrewfullard) - [#1539](https://github.com/tardis-sn/tardis/pull/1539) Add ion contributions to SDEC plotter (#1539) (@MarkMageeAstro) - [#1531](https://github.com/tardis-sn/tardis/pull/1531) Fix issue 1485 SDEC label bugs (#1531) (@atharva-2001) - [#1493](https://github.com/tardis-sn/tardis/pull/1493) Added workflow for Documentation preview generation (#1493) (@aribalam) - [#1540](https://github.com/tardis-sn/tardis/pull/1540) fix version number displayed in docs (#1540) (@epassaro) - [#1538](https://github.com/tardis-sn/tardis/pull/1538) clean template files (#1538) (@epassaro) - [#1512](https://github.com/tardis-sn/tardis/pull/1512) Change the default number of interpolate_shells for the formal integral (#1512) (@chvogl) - [#1499](https://github.com/tardis-sn/tardis/pull/1499) Enable full tests for Formal Integral (#1499) (@aribalam) - [#1530](https://github.com/tardis-sn/tardis/pull/1530) Typos in git_workflow guide (#1530) (@Molkree) - [#1535](https://github.com/tardis-sn/tardis/pull/1535) Fix macOS tests (pickle protocol 5) (#1535) (@epassaro) - [#1478](https://github.com/tardis-sn/tardis/pull/1478) Create a symlink of tardis_example.yml (#1478) (@yuyizheng1112) - [#1527](https://github.com/tardis-sn/tardis/pull/1527) rtd-theme is incompatible with docutils 0.17 (#1527) (@atharva-2001) - [#1526](https://github.com/tardis-sn/tardis/pull/1526) enable manual trigger for docs (#1526) (@epassaro) - [#1517](https://github.com/tardis-sn/tardis/pull/1517) Add catch for missing elements in SDEC plot (#1517) (@MarkMageeAstro) - [#1483](https://github.com/tardis-sn/tardis/pull/1483) corrected_csvy_model_files (#1483) (@antreev-brar) - [#1479](https://github.com/tardis-sn/tardis/pull/1479) getting rid of PerformanceWarning: indexing past lexsort depth may impact performance. (#1479) (@atharva-2001) - [#1506](https://github.com/tardis-sn/tardis/pull/1506) Add ability to plot only top contributing elements to SDEC plot (#1506) (@MarkMageeAstro) - [#1509](https://github.com/tardis-sn/tardis/pull/1509) Collisional ionization (#1509) (@chvogl) - [#1477](https://github.com/tardis-sn/tardis/pull/1477) added option for keyword arguments in spectrum plot function (#1477) (@aribalam) - [#1474](https://github.com/tardis-sn/tardis/pull/1474) Updated Z value of O (#1474) (@ankur-soni97) - [#1498](https://github.com/tardis-sn/tardis/pull/1498) Feature request: add virtual-packet-logging option to run_tardis() (#1498) (@yuyizheng1112) - [#1502](https://github.com/tardis-sn/tardis/pull/1502) add missing / in .coveragerc file (#1502) (@yuyizheng1112) - [#1492](https://github.com/tardis-sn/tardis/pull/1492) Fix docstring mistakes in #1145 (#1492) (@chvogl) - [#1505](https://github.com/tardis-sn/tardis/pull/1505) Fixing hyperlink (#1505) (@KevinCawley) - [#1481](https://github.com/tardis-sn/tardis/pull/1481) Added Documentation for Parallel execution with Numba and OpenMP (#1481) (@aribalam) - [#1145](https://github.com/tardis-sn/tardis/pull/1145) Add photoionization-related rates (#1145) (@chvogl) - [#1470](https://github.com/tardis-sn/tardis/pull/1470) Incorporating old physics section of the documentation (#1470) (@smithis7) - [#1459](https://github.com/tardis-sn/tardis/pull/1459) Removed the deprecated --with-vpacket-logging flag (#1459) (@antreev-brar) - [#1462](https://github.com/tardis-sn/tardis/pull/1462) Renamed widgets subpackage to visualization and restructured modules within it (#1462) (@jaladh-singhal) - [#1464](https://github.com/tardis-sn/tardis/pull/1464) Fix the array types when interpolate_shells > 0 (@Rodot-) - [#1454](https://github.com/tardis-sn/tardis/pull/1454) Reorganizing Models (#1454) (@smithis7) - [#1458](https://github.com/tardis-sn/tardis/pull/1458) Added option to create redirects in docs configuration and redirected gui to visualization (#1458) (@jaladh-singhal) - [#1457](https://github.com/tardis-sn/tardis/pull/1457) Reproduced SDEC plots in demo notebook (@jaladh-singhal) - [#1446](https://github.com/tardis-sn/tardis/pull/1446) Fixed italicised Units in sdec_plot (#1446) (@DhruvSondhi) - [#1438](https://github.com/tardis-sn/tardis/pull/1438) Add documentation for Spectral Element Decomposition Plot (#1438) (@jaladh-singhal) - [#1455](https://github.com/tardis-sn/tardis/pull/1455) numba_warning (#1455) (@antreev-brar) - [#1442](https://github.com/tardis-sn/tardis/pull/1442) Fixed distance parameter not producing accurate SDEC plots (#1442) (@jaladh-singhal) - [#1432](https://github.com/tardis-sn/tardis/pull/1432) fix update changelog workflow (#1432) (@epassaro) - [#1441](https://github.com/tardis-sn/tardis/pull/1441) Rename SEDec to SDEC in Spectral element DEComposition plot (#1441) (@jaladh-singhal) - [#1430](https://github.com/tardis-sn/tardis/pull/1430) compare refdata with arbitrary labels (#1430) (@epassaro) - [#1431](https://github.com/tardis-sn/tardis/pull/1431) Documentation guidelines hotfix (#1431) (@KevinCawley) - [#1424](https://github.com/tardis-sn/tardis/pull/1424) Rename Kromer Plot to Spectral Element Decomposition (SEDec) Plot (#1424) (@jaladh-singhal) - [#1409](https://github.com/tardis-sn/tardis/pull/1409) add docstr-coverage workflow (#1409) (@epassaro) ### v3.0.dev3801 (2021/01/08 21:28 +00:00) - [#1393](https://github.com/tardis-sn/tardis/pull/1393) update env file (#1393) (@epassaro) ### v3.0.dev3794 (2020/12/21 15:22 +00:00) - [#1241](https://github.com/tardis-sn/tardis/pull/1241) Add modified Kromer plot to work with widgets (@jaladh-singhal) ### v3.0.dev3769 (2020/12/18 21:07 +00:00) - [#1395](https://github.com/tardis-sn/tardis/pull/1395) Update Matterbridge docs (#1395) (@epassaro) - [#1369](https://github.com/tardis-sn/tardis/pull/1369) Fix incorrect docstrings (#1369) (@KevinCawley) - [#1383](https://github.com/tardis-sn/tardis/pull/1383) add preview docs section (#1383) (@epassaro) - [#1392](https://github.com/tardis-sn/tardis/pull/1392) Fix documentation build (#1392) (@epassaro) - [#1387](https://github.com/tardis-sn/tardis/pull/1387) Revert "Fixing docs building problem (#1387)" (#1394) (@andrewfullard) - [#1387](https://github.com/tardis-sn/tardis/pull/1387) Fixing docs building problem (#1387) (@smithis7) - [#1380](https://github.com/tardis-sn/tardis/pull/1380) Packet logging fixes for visualization (@andrewfullard) - [#1384](https://github.com/tardis-sn/tardis/pull/1384) Small fixes for existing workflows (#1384) (@epassaro) ### v3.0.dev3756 (2020/12/11 19:43 +00:00) - [#1382](https://github.com/tardis-sn/tardis/pull/1382) Fixing Quickstart Problem (@smithis7) - [#1379](https://github.com/tardis-sn/tardis/pull/1379) Reorganizing files in docs (2/2) (@smithis7) - [#1378](https://github.com/tardis-sn/tardis/pull/1378) Adding Plasma File in TOC (@smithis7) - [#1371](https://github.com/tardis-sn/tardis/pull/1371) Reorganizing files in docs (1/2) (@smithis7) - [#1372](https://github.com/tardis-sn/tardis/pull/1372) Update CI doc section (#1372) (@epassaro) - [#1375](https://github.com/tardis-sn/tardis/pull/1375) Fixed real packet logging of properties (@andrewfullard) - [#1354](https://github.com/tardis-sn/tardis/pull/1354) Virtual packet logging fix (@andrewfullard, @wkerzendorf, @Rodot-, @chvogl, @arjunsavel) - [#1368](https://github.com/tardis-sn/tardis/pull/1368) Fix of Issue #1176 (@KevinCawley) - [#1365](https://github.com/tardis-sn/tardis/pull/1365) Parallel numba setup (@andrewfullard, @wkerzendorf, @Rodot-, @chvogl, @arjunsavel) - [#1331](https://github.com/tardis-sn/tardis/pull/1331) Update changelog workflow (@epassaro) ### v3.0.dev3698 (2020/12/04 19:50 +00:00) - [#1366](https://github.com/tardis-sn/tardis/pull/1366) Fix duplicate appending of scalars in HDF writer and add an overwrite option (@jaladh-singhal) - [#1364](https://github.com/tardis-sn/tardis/pull/1364) Fixing issue #1357 (@smithis7) - [#1359](https://github.com/tardis-sn/tardis/pull/1359) Fix of Issue #680 (#1359) (@KevinCawley) - [#1361](https://github.com/tardis-sn/tardis/pull/1361) Fixing issue #1177 (#1361) (@smithis7) ### v3.0.dev3680 (2020/11/25 18:38 +00:00) - [#1358](https://github.com/tardis-sn/tardis/pull/1358) Fix C formal integral (@andrewfullard, @chvogl) - [#4](https://github.com/tardis-sn/tardis/pull/4) Fixed two random indentation irregularities found upon review (@KevinCawley) - [#3](https://github.com/tardis-sn/tardis/pull/3) Fixed the last file for #680 (@KevinCawley) - [#2](https://github.com/tardis-sn/tardis/pull/2) Fixing Issue #680 (@KevinCawley) ### v3.0.dev3673 (2020/11/18 16:26 +00:00) - [#1353](https://github.com/tardis-sn/tardis/pull/1353) fix doc workflow (@epassaro) - [#1349](https://github.com/tardis-sn/tardis/pull/1349) Adding documentation for research articles that used TARDIS (@KevinCawley) - [#929](https://github.com/tardis-sn/tardis/pull/929) This is a year worth of work from many people and hopefully will make TARDIS easier to use and develop on. Co-authored-by: Andrew Fullard Co-authored-by: Jack O'Brien Co-authored-by: Christian Vogl Co-authored-by: Andreas Flörs Co-authored-by: Luke Shingles Co-authored-by: Alice Harpole Co-authored-by: Marc Williamson Co-authored-by: Yssa Camacho Co-authored-by: Arjun Savel Co-authored-by: Stuart Archibald Co-authored-by: Siu Kwan Lam (@andrewfullard, @wkerzendorf, @Rodot-, @chvogl, @arjunsavel) - [#929](https://github.com/tardis-sn/tardis/pull/929) Numba montecarlo (@andrewfullard, @wkerzendorf, @Rodot-, @chvogl, @arjunsavel) - [#1](https://github.com/tardis-sn/tardis/pull/1) Updating my Version of Tardis and Fixing Environment (@wkerzendorf, @epassaro, @jaladh-singhal, @morganlee123, @Ak0303, @arjunsavel) ### v3.0.dev3541 (2020/11/10 18:45 +00:00) - [#1340](https://github.com/tardis-sn/tardis/pull/1340) Moved staticmethods of line_info module to a dedicated plot_util module (@jaladh-singhal) ### v3.0.dev3539 (2020/11/04 16:50 +00:00) - [#1333](https://github.com/tardis-sn/tardis/pull/1333) Rename testing pipeline (#1333) (@epassaro) - [#1300](https://github.com/tardis-sn/tardis/pull/1300) Remove pip install option from installation docs (#1300) (@jaladh-singhal) - [#1330](https://github.com/tardis-sn/tardis/pull/1330) Small fix for release pipeline (#1330) (@epassaro) - [#1332](https://github.com/tardis-sn/tardis/pull/1332) Remove helper scripts (#1332) (@epassaro) - [#1335](https://github.com/tardis-sn/tardis/pull/1335) Updated gitignore to ignore auto-generated files (#1335) (@jaladh-singhal) - [#1326](https://github.com/tardis-sn/tardis/pull/1326) Add workflow for autodeploying documentation to github pages via an action (#1326) (@morganlee123) - [#1319](https://github.com/tardis-sn/tardis/pull/1319) Numba montecarlo tests merged (#1319) (@chvogl) - [#1283](https://github.com/tardis-sn/tardis/pull/1283) Changed latex strings to raw strings (#1283) (@Ak0303) - [#1310](https://github.com/tardis-sn/tardis/pull/1310) Apply new template to refdata pipeline (#1310) (@epassaro) - [#1308](https://github.com/tardis-sn/tardis/pull/1308) Apply new template to release pipeline (#1308) (@epassaro) - [#1318](https://github.com/tardis-sn/tardis/pull/1318) Numba montecarlo profile1 (@wkerzendorf) - [#1317](https://github.com/tardis-sn/tardis/pull/1317) Fixed `calculate_distance_line` showing nu_diff < 0 (#1317) (@Rodot-) - [#1309](https://github.com/tardis-sn/tardis/pull/1309) Re-add C formal integral (#1309) (@chvogl) ### v3.0.dev3527 (2020/10/05 16:43 +00:00) - [#1313](https://github.com/tardis-sn/tardis/pull/1313) Create FUNDING.yml (#1313) (@jaladh-singhal) ### v3.0.dev3526 (2020/10/01 09:50 +00:00) - [#1312](https://github.com/tardis-sn/tardis/pull/1312) Initial commit (#1312) (@epassaro) - [#1274](https://github.com/tardis-sn/tardis/pull/1274) Add space to plasma error message (@arjunsavel) - [#1280](https://github.com/tardis-sn/tardis/pull/1280) Add widgets documentation to tardis docs (@jaladh-singhal) ### v3.0.dev3510 (2020/09/25 15:56 +00:00) - [#1299](https://github.com/tardis-sn/tardis/pull/1299) Model configuration output in HDF (#1299) (@andrewfullard) - [#1304](https://github.com/tardis-sn/tardis/pull/1304) Use tardis-refdata from Azure mirror (CI/CD) (#1304) (@epassaro) - [#1264](https://github.com/tardis-sn/tardis/pull/1264) Add line info widget to widgets subpackage (#1264) (@jaladh-singhal) ### v3.0.dev3504 (2020/09/09 10:16 +00:00) - [#1296](https://github.com/tardis-sn/tardis/pull/1296) Pin pyne to 0.7.0 (#1296) (@andrewfullard) ### v3.0.dev3503 (2020/09/04 09:18 +00:00) - [#1291](https://github.com/tardis-sn/tardis/pull/1291) Download atom data from opensupernova mirror (#1291) (@epassaro) - [#1285](https://github.com/tardis-sn/tardis/pull/1285) Final numba PR (#1285) (@arjunsavel) - [#1254](https://github.com/tardis-sn/tardis/pull/1254) Fix how virtual_packet properties are saved in hdf (#1254) (@jaladh-singhal) - [#1278](https://github.com/tardis-sn/tardis/pull/1278) Pin numpy to v1.17 (#1278) (@epassaro) ### v3.0.dev3500 (2020/08/12 09:52 +00:00) - [#1271](https://github.com/tardis-sn/tardis/pull/1271) Pin numpy to v1.19.0 (#1271) (@epassaro) - [#1266](https://github.com/tardis-sn/tardis/pull/1266) Move to Pandas 1.x (#1266) (@epassaro) - [#1244](https://github.com/tardis-sn/tardis/pull/1244) Explicitly pass number of vpackets to montecarlo_main_loop (#1244) (@arjunsavel) - [#1235](https://github.com/tardis-sn/tardis/pull/1235) test and fix for issue #1228 (#1235) (@jordi5) ### v3.0.dev3497 (2020/08/07 15:26 +00:00) - [#1267](https://github.com/tardis-sn/tardis/pull/1267) Temporarily fetch refdata from GDrive (#1267) (@epassaro) - [#1265](https://github.com/tardis-sn/tardis/pull/1265) add GIT_LFS_SMUDGE (#1265) (@kaushik94) - [#1262](https://github.com/tardis-sn/tardis/pull/1262) Update package versions (#1262) (@epassaro) - [#1263](https://github.com/tardis-sn/tardis/pull/1263) Clean up status badge display (#1263) (@chvogl) - [#1261](https://github.com/tardis-sn/tardis/pull/1261) Add governance document (#1261) (@wkerzendorf) ### v3.0.dev3487 (2020/07/30 22:18 +00:00) - [#1259](https://github.com/tardis-sn/tardis/pull/1259) emphasised reporting guidelines in code of conduct (#1259) (@harpolea) - [#1255](https://github.com/tardis-sn/tardis/pull/1255) Pin pyne to v0.5 (#1255) (@epassaro) - [#1213](https://github.com/tardis-sn/tardis/pull/1213) Re-applied Black formatting to tardis after excluding undesired directories (#1213) (@jaladh-singhal) ### v3.0.dev3484 (2020/07/19 14:30 +00:00) - [#1210](https://github.com/tardis-sn/tardis/pull/1210) [MRG] Using Mamba in Pipelines (#1210) (@kaushik94) - [#1237](https://github.com/tardis-sn/tardis/pull/1237) Add new Contribution guidelines (#1237) (@jaladh-singhal) - [#1238](https://github.com/tardis-sn/tardis/pull/1238) code of conduct symlink (#1238) (@wkerzendorf) - [#1234](https://github.com/tardis-sn/tardis/pull/1234) TARDIS Code of Conduct (#1234) (@wkerzendorf) - [#1233](https://github.com/tardis-sn/tardis/pull/1233) Update of the Governance model (#1233) (@wkerzendorf) - [#1231](https://github.com/tardis-sn/tardis/pull/1231) Roadmap Documentation Page (#1231) (@marxwillia) - [#1227](https://github.com/tardis-sn/tardis/pull/1227) Update base.py (#1227) (@arjunsavel) ### v3.0.dev3477 (2020/07/09 03:06 +00:00) - [#1218](https://github.com/tardis-sn/tardis/pull/1218) Move and rename coverage file (#1218) (@arjunsavel) - [#1224](https://github.com/tardis-sn/tardis/pull/1224) Added better mission statement (@wkerzendorf) - [#1190](https://github.com/tardis-sn/tardis/pull/1190) Change `pytestconfig` to `request.config` (#1190) (@epassaro) - [#1219](https://github.com/tardis-sn/tardis/pull/1219) Update index.rst (#1219) (@ycamacho) - [#1136](https://github.com/tardis-sn/tardis/pull/1136) Debugging relativity on numba_montecarlo (#1136) (@arjunsavel) ### v3.0.dev3472 (2020/06/27 20:11 +00:00) - [#1203](https://github.com/tardis-sn/tardis/pull/1203) Minor changes to the environment file and cleanup (#1203) (@epassaro) - [#1209](https://github.com/tardis-sn/tardis/pull/1209) add sashank27 orcid (#1209) (@sashank27) - [#1207](https://github.com/tardis-sn/tardis/pull/1207) add git-blame-ignore for code style black Changes (#1207) (@wkerzendorf) - [#1201](https://github.com/tardis-sn/tardis/pull/1201) Code style black (#1201) (@wkerzendorf) - [#1200](https://github.com/tardis-sn/tardis/pull/1200) Added jaladh-singhal's orcid (#1200) (@jaladh-singhal) - [#1197](https://github.com/tardis-sn/tardis/pull/1197) add arjun's name to the ORCID list (#1197) (@arjunsavel) - [#1166](https://github.com/tardis-sn/tardis/pull/1166) Create a new subpackage for jupyter-widgets and add shell info widgets (#1166) (@jaladh-singhal) ### v3.0.dev3463 (2020/06/19 22:51 +00:00) - [#1195](https://github.com/tardis-sn/tardis/pull/1195) Fix badges in README.rst (#1195) (@epassaro) - [#1193](https://github.com/tardis-sn/tardis/pull/1193) Unpin astropy version (#1193) (@epassaro) - [#1191](https://github.com/tardis-sn/tardis/pull/1191) Add note to tell users which OS are supported (issue #1125) (#1191) (@jordi5) - [#1158](https://github.com/tardis-sn/tardis/pull/1158) Make consistency edits to documentation (#1158) (@arjunsavel) ### v3.0.dev3459 (2020/06/12 18:01 +00:00) - [#1185](https://github.com/tardis-sn/tardis/pull/1185) Upgrade pytest version (#1185) (@epassaro) ### v3.0.dev3458 (2020/06/02 19:11 +00:00) - [#1180](https://github.com/tardis-sn/tardis/pull/1180) Remove test pipeline (#1180) (@epassaro) - [#1153](https://github.com/tardis-sn/tardis/pull/1153) update doc page to a notebook (#1153) (@sashank27) - [#1150](https://github.com/tardis-sn/tardis/pull/1150) Fix the Plasma tests (#1150) (@wkerzendorf) - [#1178](https://github.com/tardis-sn/tardis/pull/1178) Fix Jack O`Brien and Jordi Eguren author names (#1178) (@epassaro) - [#1171](https://github.com/tardis-sn/tardis/pull/1171) Changed a print from python 2 to python 3 (#1171) (@arjunsavel) - [#1165](https://github.com/tardis-sn/tardis/pull/1165) Fix callbacks in run_tardis (@Rodot-) ### v3.0.dev3448 (2020/05/28 17:08 +00:00) - [#1173](https://github.com/tardis-sn/tardis/pull/1173) Fix GUI and plasma tests (@epassaro) - [#1168](https://github.com/tardis-sn/tardis/pull/1168) add checkpoint to PR template checklist (#1168) (@harpolea) - [#1162](https://github.com/tardis-sn/tardis/pull/1162) Remove duplicated export (#1162) (@epassaro) ### v3.0.dev3442 (2020/05/21 23:34 +00:00) - [#1159](https://github.com/tardis-sn/tardis/pull/1159) Fixed crash when integrating in parallel. Crash was previously caused by a double free error. Removing the last call to free caused the spectrum to be computed incorrectly, indicating that the structure of the parallelism was at fault. I removed the firstprivate declaration from the first call to omp parallel as there was no need to make copies of the pointers for each thread (was this even a reasonable thing to do since each thread would have to reallocate the arrays anyway?). There also did not appear to be any need to maintain copies of L or exp_tau for each thread. I then moved the last call to free outside of the parallel section. So now there is no memory allocation or deallocation of L or exp_tau in a parallel block, and exp_tau is freed only once as it should be (#1159) (@Rodot-) - [#1155](https://github.com/tardis-sn/tardis/pull/1155) add codecov to azure pipelines (#1155) (@wkerzendorf) - [#1157](https://github.com/tardis-sn/tardis/pull/1157) Update .mailmap (#1157) (@epassaro) ### v3.0.dev3439 (2020/05/20 13:25 +00:00) - [#1142](https://github.com/tardis-sn/tardis/pull/1142) Split release pipeline (#1142) (@epassaro) - [#1151](https://github.com/tardis-sn/tardis/pull/1151) Git ignored VSCode specific files (#1151) (@jaladh-singhal) - [#1149](https://github.com/tardis-sn/tardis/pull/1149) Made plot size larger in quickstart notebook (#1149) (@jaladh-singhal) - [#1147](https://github.com/tardis-sn/tardis/pull/1147) allow downloading of example file in quickstart (#1147) (@sashank27) - [#1105](https://github.com/tardis-sn/tardis/pull/1105) Add skip condition if QT_API is no set (issue #1101) (@jordi5) - [#1143](https://github.com/tardis-sn/tardis/pull/1143) Set manual trigger on file (compare refdata) (@epassaro) - [#1144](https://github.com/tardis-sn/tardis/pull/1144) add option to execute quickstart in build (#1144) (@sashank27) ### v3.0.dev3424 (2020/05/07 15:29 +00:00) - [#1133](https://github.com/tardis-sn/tardis/pull/1133) Solve pending issues of the release pipeline (#1133) (@epassaro) - [#1141](https://github.com/tardis-sn/tardis/pull/1141) fix warnings in quickstart (#1141) (@sashank27) - [#1137](https://github.com/tardis-sn/tardis/pull/1137) Increasing glob-like omission of coverage files (#1137) (@arjunsavel) - [#1139](https://github.com/tardis-sn/tardis/pull/1139) Added more file types to git ignore (#1139) (@jaladh-singhal) - [#1134](https://github.com/tardis-sn/tardis/pull/1134) Update mailmap (@epassaro) - [#1135](https://github.com/tardis-sn/tardis/pull/1135) Running tests on MacOS-10.14 (@epassaro) - [#1068](https://github.com/tardis-sn/tardis/pull/1068) Migrate gui to PyQt5 (issue #988) (#1068) (@jordi5) - [#1085](https://github.com/tardis-sn/tardis/pull/1085) Solves issue #680 for tardis.util.base (i.e. numpydocs format for doc strings.) (@Phantsure) - [#1055](https://github.com/tardis-sn/tardis/pull/1055) renamed capmanager class functions (#1055) (@not4win) - [#1048](https://github.com/tardis-sn/tardis/pull/1048) Re-activate TARDIS tests (#1048) (@epassaro) ### v3.0.dev3409 (2020/02/25 04:02 +00:00) - [#1046](https://github.com/tardis-sn/tardis/pull/1046) Updated zenodo.json (#1046) (@epassaro) - [#1045](https://github.com/tardis-sn/tardis/pull/1045) Fix file paths at `diff` step in release pipeline (#1045) (@epassaro) - [#1040](https://github.com/tardis-sn/tardis/pull/1040) Re-activate release job (#1040) (@epassaro) - [#1039](https://github.com/tardis-sn/tardis/pull/1039) Update .mailmap (#1039) (@epassaro) ### v3.0.dev3403 (2020/02/19 15:55 +00:00) - [#1031](https://github.com/tardis-sn/tardis/pull/1031) Create Zenodo JSON file (#1031) (@epassaro) - [#1036](https://github.com/tardis-sn/tardis/pull/1036) Update zenodo.json (#1036) (@epassaro) - [#1035](https://github.com/tardis-sn/tardis/pull/1035) Update .mailmap (#1035) (@epassaro) - [#1034](https://github.com/tardis-sn/tardis/pull/1034) Update .mailmap (#1034) (@epassaro) - [#1032](https://github.com/tardis-sn/tardis/pull/1032) Add Mark Magee to .mailmap (#1032) (@epassaro) - [#1025](https://github.com/tardis-sn/tardis/pull/1025) Add `compilers` to environment YAML file (#1025) (@epassaro) - [#1026](https://github.com/tardis-sn/tardis/pull/1026) Minor changes (#1026) (@epassaro) ### 3.0.dev3396 (2020/02/07 15:00 +00:00) - [#1027](https://github.com/tardis-sn/tardis/pull/1027) Added Mark Magee (#1027) (@MarkMageeAstro) - [#1024](https://github.com/tardis-sn/tardis/pull/1024) Add epassaro orcid (#1024) (@epassaro) - [#1022](https://github.com/tardis-sn/tardis/pull/1022) added Alice's orcid (#1022) (@harpolea) ### 3.0.dev3384 (2020/02/02 21:56 +00:00) - [#1021](https://github.com/tardis-sn/tardis/pull/1021) Set cron job, disable CI and PR (#1021) (@epassaro) ### 3.0.dev3383 (2020/02/02 19:01 +00:00) - [#1015](https://github.com/tardis-sn/tardis/pull/1015) Set up release TARDIS version with Azure Pipelines (#1015) (@epassaro) - [#1020](https://github.com/tardis-sn/tardis/pull/1020) Update .mailmap (#1020) (@livnehra) - [#1018](https://github.com/tardis-sn/tardis/pull/1018) Updated .mailmap (#1018) (@epassaro) - [#1010](https://github.com/tardis-sn/tardis/pull/1010) Pipeline for comparing reference data (#1010) (@epassaro) - [#1016](https://github.com/tardis-sn/tardis/pull/1016) Removed GH Action for release versions (#1016) (@epassaro) ### 3.0.dev3388 (2020/01/25 22:36 +00:00) - [#1013](https://github.com/tardis-sn/tardis/pull/1013) Fixed typo (#1013) (@epassaro) - [#1006](https://github.com/tardis-sn/tardis/pull/1006) Trying to get the right version number for automatic release (#1006) (@epassaro) - [#1008](https://github.com/tardis-sn/tardis/pull/1008) Improvements for the update_reference section [docs] (#1008) (@epassaro) - [#1011](https://github.com/tardis-sn/tardis/pull/1011) Gui fix (#1011) (@marxwillia) - [#1009](https://github.com/tardis-sn/tardis/pull/1009) Fix for packet source unit test (#1009) (@epassaro) - [#1007](https://github.com/tardis-sn/tardis/pull/1007) Fix for vboundary tests (#1007) (@epassaro) - [#995](https://github.com/tardis-sn/tardis/pull/995) Checking failing tests on Azure (#995) (@kaushik94) - [#1005](https://github.com/tardis-sn/tardis/pull/1005) Add YML file for release version (#1005) (@epassaro) - [#1004](https://github.com/tardis-sn/tardis/pull/1004) Fixed csvy abundance indexing bug (#1004) (@marxwillia) - [#1003](https://github.com/tardis-sn/tardis/pull/1003) Custom source packets (#1003) (@marxwillia) - [#994](https://github.com/tardis-sn/tardis/pull/994) Large cleanup operation (#994) (@wkerzendorf) - [#992](https://github.com/tardis-sn/tardis/pull/992) Changes made to update_refdata documentation (#992) (@kowal180) - [#967](https://github.com/tardis-sn/tardis/pull/967) log additional properties in hdf witeout when --with-vpacket-logging is present (#967) (@kaushik94) - [#969](https://github.com/tardis-sn/tardis/pull/969) Fixes numpydoc for util (#969) (@kowal180) - [#985](https://github.com/tardis-sn/tardis/pull/985) Fix typo (#985) (@jreichenbach-msu) - [#983](https://github.com/tardis-sn/tardis/pull/983) Fix git clone rendering in installation (#983) (@jreichenbach-msu) - [#982](https://github.com/tardis-sn/tardis/pull/982) Pinned `numpy` to v1.15 (#982) (@epassaro) - [#978](https://github.com/tardis-sn/tardis/pull/978) Add further fix to quickstart link (#978) (@jreichenbach-msu) - [#975](https://github.com/tardis-sn/tardis/pull/975) Add links to Quickstart (#975) (@jreichenbach-msu) - [#971](https://github.com/tardis-sn/tardis/pull/971) Fix formal integral spikes bug (see #970) (#971) (@chvogl) - [#968](https://github.com/tardis-sn/tardis/pull/968) Fixed GUI #950 tardis/gui/widgets.py (@jamesgillanders) - [#965](https://github.com/tardis-sn/tardis/pull/965) Isotope time0 (#965) (@marxwillia) - [#966](https://github.com/tardis-sn/tardis/pull/966) fix AtomData repr. (#966) (@wkerzendorf) - [#964](https://github.com/tardis-sn/tardis/pull/964) Raise error if requested atoms are not in the atomic data (#964) (@chvogl) - [#959](https://github.com/tardis-sn/tardis/pull/959) Csvy model config dict (#959) (@marxwillia) - [#949](https://github.com/tardis-sn/tardis/pull/949) Add issue template (#949) (@Youssef15015) - [#960](https://github.com/tardis-sn/tardis/pull/960) Save integrated spectrum to hdf if requested (#960) (@chvogl) - [#957](https://github.com/tardis-sn/tardis/pull/957) add blondin converter (#957) (@wkerzendorf) - [#956](https://github.com/tardis-sn/tardis/pull/956) Dilution factor fix (#956) (@marxwillia) - [#953](https://github.com/tardis-sn/tardis/pull/953) add code comparison (#953) (@wkerzendorf) - [#952](https://github.com/tardis-sn/tardis/pull/952) Base schema fix (#952) (@marxwillia) - [#951](https://github.com/tardis-sn/tardis/pull/951) Documentation restructure (@wkerzendorf, @marxwillia) - [#26](https://github.com/tardis-sn/tardis/pull/26) Added Model Doc Page (#26) (@marxwillia) - [#943](https://github.com/tardis-sn/tardis/pull/943) Update General CI Documentation (#943) (@Youssef15015) - [#936](https://github.com/tardis-sn/tardis/pull/936) csvy_model (@Youssef15015, @marxwillia) - [#940](https://github.com/tardis-sn/tardis/pull/940) parent 8d9001822f586857f2f8353a56185310832886dc (@Youssef15015) - [#942](https://github.com/tardis-sn/tardis/pull/942) Update self-hossted agent documentaiton (#942) (@Youssef15015) - [#946](https://github.com/tardis-sn/tardis/pull/946) Update build documentation script (@Youssef15015) - [#945](https://github.com/tardis-sn/tardis/pull/945) Revert "Remove PR Trigger" (@wkerzendorf) - [#944](https://github.com/tardis-sn/tardis/pull/944) Remove PR Trigger (@Youssef15015) - [#939](https://github.com/tardis-sn/tardis/pull/939) Deploying documentation using Azure (@Youssef15015) - [#940](https://github.com/tardis-sn/tardis/pull/940) Correct index script spelling (#940) (@Youssef15015) - [#928](https://github.com/tardis-sn/tardis/pull/928) Added csvy parser (#928) (@marxwillia) - [#933](https://github.com/tardis-sn/tardis/pull/933) Radiative recombination (#933) (@chvogl) - [#934](https://github.com/tardis-sn/tardis/pull/934) Relocated the azure_pipelines.yml into a new directory called pipelines, and renamed it as pipeline_A (#934) (@Youssef15015) ### v3.0-alpha.3 (2019/05/13 22:05 +00:00) - [#930](https://github.com/tardis-sn/tardis/pull/930) Fix for conda-forge package (#930) (@epassaro) - [#918](https://github.com/tardis-sn/tardis/pull/918) Density docs (#918) (@marxwillia) - [#926](https://github.com/tardis-sn/tardis/pull/926) Adding a TARDIS data repo (#926) (@wkerzendorf) - [#924](https://github.com/tardis-sn/tardis/pull/924) Migrate beta_sobolev calculation from cython to numba (#924) (@chvogl) - [#925](https://github.com/tardis-sn/tardis/pull/925) Docs/fix changelog (@wkerzendorf) - [#923](https://github.com/tardis-sn/tardis/pull/923) Fix nlte normalization (@livnehra) - [#920](https://github.com/tardis-sn/tardis/pull/920) Revert "Fix nlte normalization (#920)" (#922) (@wkerzendorf) - [#920](https://github.com/tardis-sn/tardis/pull/920) Fix nlte normalization (#920) (@wkerzendorf) - [#921](https://github.com/tardis-sn/tardis/pull/921) add changes builder to travis process (#921) (@wkerzendorf) - [#919](https://github.com/tardis-sn/tardis/pull/919) Add possibility to bias vpacket emission based on optical depth (#919) (@chvogl) - [#914](https://github.com/tardis-sn/tardis/pull/914) make python3 compatible (#914) (@wkerzendorf) - [#902](https://github.com/tardis-sn/tardis/pull/902) general overhaul of the docs for 3.0 (#902) (@wkerzendorf) - [#916](https://github.com/tardis-sn/tardis/pull/916) make python3 compatible (#916) (@wkerzendorf) - [#915](https://github.com/tardis-sn/tardis/pull/915) Parsing STELLA files for TARDIS (#915) (@sarafina325) - [#911](https://github.com/tardis-sn/tardis/pull/911) Use Russian roulette to kill v-packets with negligible weight (#911) (@chvogl) - [#697](https://github.com/tardis-sn/tardis/pull/697) Relativity (#697) (@chvogl) ### v3.0.a1 (2019/03/10 15:03 +00:00) - [#901](https://github.com/tardis-sn/tardis/pull/901) .nojekyll added to docs (#901) (@debajyotidasgupta) - [#897](https://github.com/tardis-sn/tardis/pull/897) add pytest azurepipelines (#897) (@wkerzendorf) - [#896](https://github.com/tardis-sn/tardis/pull/896) Adding general build artefacts (#896) (@wkerzendorf) - [#894](https://github.com/tardis-sn/tardis/pull/894) Azure pipeline for TARDIS (#894) (@wkerzendorf) - [#893](https://github.com/tardis-sn/tardis/pull/893) add doctr to TARDIS (#893) (@wkerzendorf) - [#892](https://github.com/tardis-sn/tardis/pull/892) adding azure-pipelines (#892) (@wkerzendorf) - [#891](https://github.com/tardis-sn/tardis/pull/891) New template setup from astropy (#891) (@wkerzendorf) - [#888](https://github.com/tardis-sn/tardis/pull/888) Update installation.rst (#888) (@nileshpatra) - [#886](https://github.com/tardis-sn/tardis/pull/886) Pandas ix fix (#886) (@wkerzendorf) - [#879](https://github.com/tardis-sn/tardis/pull/879) Python3 version of TARDIS (#879) (@wkerzendorf) - [#881](https://github.com/tardis-sn/tardis/pull/881) Adds description of gcc problem to documentation (#881) (@ycamacho) - [#859](https://github.com/tardis-sn/tardis/pull/859) Use interpolated values to do formal integral with more shells (#859) (@chvogl) - [#873](https://github.com/tardis-sn/tardis/pull/873) Some small fixes related to the documentation and the building process (Fix #842) (#873) (@unoebauer) - [#868](https://github.com/tardis-sn/tardis/pull/868) Add Travis Stages: Activate Integration tests (#868) (@unoebauer) - [#866](https://github.com/tardis-sn/tardis/pull/866) Add Travis Caching and separate scripts for CI (#866) (@wkerzendorf) - [#864](https://github.com/tardis-sn/tardis/pull/864) Unify unittest hdfs (#864) (@unoebauer) - [#865](https://github.com/tardis-sn/tardis/pull/865) Adding CodeCov integration (#865) (@wkerzendorf) - [#860](https://github.com/tardis-sn/tardis/pull/860) add call_back to run_tardis (#860) (@wkerzendorf) - [#863](https://github.com/tardis-sn/tardis/pull/863) Thomson cross section: Continuation of PR #688 (#863) (@unoebauer) - [#850](https://github.com/tardis-sn/tardis/pull/850) Add full test for formal integral method (#850) (@unoebauer) - [#861](https://github.com/tardis-sn/tardis/pull/861) Describe refdata update and workflow refactor (#861) (@wkerzendorf) - [#848](https://github.com/tardis-sn/tardis/pull/848) Add capability to store information about the plasma state during iterations (#848) (@unoebauer) - [#857](https://github.com/tardis-sn/tardis/pull/857) Refactor logging (#857) (@wkerzendorf) - [#856](https://github.com/tardis-sn/tardis/pull/856) Extend formal integral to line_interaction_type macroatom (#856) (@chvogl) - [#855](https://github.com/tardis-sn/tardis/pull/855) Make the conda-forge channel the only channel (#855) (@wkerzendorf) - [#853](https://github.com/tardis-sn/tardis/pull/853) Fix formal integral (#853) (@chvogl) - [#849](https://github.com/tardis-sn/tardis/pull/849) Missing refdata (#849) (@wkerzendorf) - [#851](https://github.com/tardis-sn/tardis/pull/851) add atomic data description (#851) (@wkerzendorf) - [#845](https://github.com/tardis-sn/tardis/pull/845) Update Documentation: new location of tardis_example (#845) (@unoebauer) - [#843](https://github.com/tardis-sn/tardis/pull/843) Fix issue with custom_composition reader (#843) (@unoebauer) - [#844](https://github.com/tardis-sn/tardis/pull/844) Remove bbsampling from schema file (#844) (@pfreddy) - [#837](https://github.com/tardis-sn/tardis/pull/837) Add json sphinx (#837) (@wkerzendorf) - [#841](https://github.com/tardis-sn/tardis/pull/841) Fixed indentation and position of delta_treatment in plasma/standard_plasmas.py (#841) (@Heringer-Epson) - [#838](https://github.com/tardis-sn/tardis/pull/838) fix cython version to specific commit (#838) (@wkerzendorf) - [#821](https://github.com/tardis-sn/tardis/pull/821) Simplify convergence strategies (#821) (@unoebauer) - [#833](https://github.com/tardis-sn/tardis/pull/833) restructure landing page to use notebooks (#833) (@wkerzendorf) - [#832](https://github.com/tardis-sn/tardis/pull/832) Fixes #830 (#832) (@unoebauer) ### v2_test3 (2018/06/18 20:13 +00:00) - [#829](https://github.com/tardis-sn/tardis/pull/829) build bleeding edge cython (#829) (@wkerzendorf) - [#828](https://github.com/tardis-sn/tardis/pull/828) trying to get travis to build (#828) (@wkerzendorf) - [#827](https://github.com/tardis-sn/tardis/pull/827) Update travis link to miniconda (#827) (@unoebauer) - [#826](https://github.com/tardis-sn/tardis/pull/826) Remove docu refs to tardis_example.tar.gz (#826) (@unoebauer) - [#820](https://github.com/tardis-sn/tardis/pull/820) update of mailmap (#820) (@wkerzendorf) - [#819](https://github.com/tardis-sn/tardis/pull/819) Reintroduce and update changelog (#819) (@unoebauer) - [#815](https://github.com/tardis-sn/tardis/pull/815) Update and Fix Documentation (#815) (@unoebauer) - [#816](https://github.com/tardis-sn/tardis/pull/816) Remove old and broken badges (@unoebauer) - [#814](https://github.com/tardis-sn/tardis/pull/814) Fix numpydoc problem (@wkerzendorf, @unoebauer) ### v2.0 (2018/04/05 13:03 +00:00) - [#812](https://github.com/tardis-sn/tardis/pull/812) Update of documentation (@unoebauer) - [#809](https://github.com/tardis-sn/tardis/pull/809) fix dependencies for tardis conda env (#809) (@wkerzendorf) - [#761](https://github.com/tardis-sn/tardis/pull/761) Add caching for integrated spectrum: Fix #760 (@unoebauer) - [#715](https://github.com/tardis-sn/tardis/pull/715) Merge 'generate_reference_path' and 'reference_path' in integration tests (bug #672) (@rinklejain) - [#801](https://github.com/tardis-sn/tardis/pull/801) Decay of isotopes branch (@wkerzendorf, @vg3095, @pfreddy) - [#806](https://github.com/tardis-sn/tardis/pull/806) Fix reference dictionary problem (@pfreddy) - [#803](https://github.com/tardis-sn/tardis/pull/803) include yml files in MANIFEST (@wkerzendorf) - [#802](https://github.com/tardis-sn/tardis/pull/802) Fix for PR #801 (@vg3095) - [#799](https://github.com/tardis-sn/tardis/pull/799) tardis/plasma/standard_plasmas.py: old database files warning (@laudb) - [#797](https://github.com/tardis-sn/tardis/pull/797) Minor Updates: Fixes for #521 and #699 (@unoebauer) - [#796](https://github.com/tardis-sn/tardis/pull/796) Prevent pandas SettingWithCopyWarning by copying DataFrames when slicing (@lukeshingles) - [#795](https://github.com/tardis-sn/tardis/pull/795) Force deactivate LaTeX in GUI - Fix #441 (@unoebauer) - [#793](https://github.com/tardis-sn/tardis/pull/793) Add pyside to requirements (needed for GUI) (@wkerzendorf, @unoebauer) - [#794](https://github.com/tardis-sn/tardis/pull/794) add new readthedocs.yml (@wkerzendorf) - [#792](https://github.com/tardis-sn/tardis/pull/792) Fix compatibility with networkx 2.0 (@lukeshingles) - [#791](https://github.com/tardis-sn/tardis/pull/791) Propagate changes to the line index into the GUI code (@yeganer) - [#786](https://github.com/tardis-sn/tardis/pull/786) The final carsus merge (@yeganer, @ftsamis, @mishinma) - [#782](https://github.com/tardis-sn/tardis/pull/782) Plasma write_to_tex/dot unit tests (@vg3095) - [#781](https://github.com/tardis-sn/tardis/pull/781) Omit coverage of test related files (@vg3095) - [#785](https://github.com/tardis-sn/tardis/pull/785) [DOC] Update Running tests doc (@vg3095) - [#774](https://github.com/tardis-sn/tardis/pull/774) Replace Comparison values in Plasma Unit Tests with reference HDF file (@vg3095) - [#780](https://github.com/tardis-sn/tardis/pull/780) LevelBoltzmannFactorNLTE.from_config is now a staticmethod (@yeganer) - [#778](https://github.com/tardis-sn/tardis/pull/778) Fix NLTE (@yeganer) - [#776](https://github.com/tardis-sn/tardis/pull/776) Fix compatibility bug in radiative_properties (@yeganer) - [#779](https://github.com/tardis-sn/tardis/pull/779) Save coverage report when tests use tardis-refdata (@vg3095) - [#775](https://github.com/tardis-sn/tardis/pull/775) Transition from atomic-dataset config option to tardis-refdata (@vg3095) - [#772](https://github.com/tardis-sn/tardis/pull/772) [TEP007] CMFGEN density parser (@vg3095) - [#771](https://github.com/tardis-sn/tardis/pull/771) [TEP007] Add cmfgen2tardis script (@vg3095) - [#757](https://github.com/tardis-sn/tardis/pull/757) [TEP007] Decay and merge isotopic abundance dataframe (@vg3095) - [#769](https://github.com/tardis-sn/tardis/pull/769) [TEP014] [DOC] Updated to_hdf notebook (@vg3095) - [#759](https://github.com/tardis-sn/tardis/pull/759) Formal Integral: including electron scattering (@unoebauer, @yeganer) - [#768](https://github.com/tardis-sn/tardis/pull/768) [TEP014] Simulation HDF and deprecated to_hdf cleanup. (@vg3095) - [#773](https://github.com/tardis-sn/tardis/pull/773) Update Documentation (@unoebauer) - [#767](https://github.com/tardis-sn/tardis/pull/767) [TEP007] Docs for isotope config (@vg3095) - [#764](https://github.com/tardis-sn/tardis/pull/764) [TEP007] Isotope stratified file support (@vg3095) - [#752](https://github.com/tardis-sn/tardis/pull/752) [TEP014] PlasmaWriterMixin (@vg3095) - [#748](https://github.com/tardis-sn/tardis/pull/748) [TEP014] Update Runner and Spectrum classes to use HDFWriter + Unit Tests (@vg3095) - [#762](https://github.com/tardis-sn/tardis/pull/762) [TEP007] Isotope uniform config option (@vg3095) - [#765](https://github.com/tardis-sn/tardis/pull/765) Attempt to fix up the GUI (@ssim, @unoebauer) - [#13](https://github.com/tardis-sn/tardis/pull/13) Introduce proper masking for GUI (addition to PR #765) (@unoebauer) - [#1](https://github.com/tardis-sn/tardis/pull/1) Streamline the OMP implementation (@yeganer) - [#756](https://github.com/tardis-sn/tardis/pull/756) [TEP007] [WIP] Isotope Abundances class (@vg3095, @wkerzendorf) - [#758](https://github.com/tardis-sn/tardis/pull/758) Add new version to tardis_env27 and add pyne (@wkerzendorf) - [#753](https://github.com/tardis-sn/tardis/pull/753) [TEP014][DOC] HDFWriter Documentation (@vg3095) - [#740](https://github.com/tardis-sn/tardis/pull/740) [GSoC] Formal integral Project (@yeganer) - [#747](https://github.com/tardis-sn/tardis/pull/747) [TEP014] Update Model and Density classes to use HDFWriter + Unit Tests (@vg3095) - [#750](https://github.com/tardis-sn/tardis/pull/750) [TEP005][QOL] Add MontecarloRunner.spectrum_integrated (@yeganer) - [#749](https://github.com/tardis-sn/tardis/pull/749) [TEP014] Change name of HDFWriter to HDFWriterMixin (@vg3095) - [#745](https://github.com/tardis-sn/tardis/pull/745) [TEP005][DOC] Documentation (@yeganer) - [#751](https://github.com/tardis-sn/tardis/pull/751) [QOL] Add default axis to TARDISSpectrum.plot (@yeganer) - [#743](https://github.com/tardis-sn/tardis/pull/743) Fix bug in plasma (@yeganer) - [#744](https://github.com/tardis-sn/tardis/pull/744) [TEP014] Added HDFWriter class + Unit Tests (@vg3095) - [#746](https://github.com/tardis-sn/tardis/pull/746) [TEP005][CONFIG] Prevent incompatible configurations (@yeganer) - [#741](https://github.com/tardis-sn/tardis/pull/741) Add unit tests for the formal integral (@yeganer) - [#742](https://github.com/tardis-sn/tardis/pull/742) Fix clash in RTD dependencies (@yeganer) - [#735](https://github.com/tardis-sn/tardis/pull/735) Move common ctest fixtures into conftest.py (@yeganer) - [#729](https://github.com/tardis-sn/tardis/pull/729) Refactor spectrum (@yeganer) - [#730](https://github.com/tardis-sn/tardis/pull/730) Fix test_plasma_simple not skipping properly (@yeganer) - [#712](https://github.com/tardis-sn/tardis/pull/712) Colorize Logger (@vg3095) - [#718](https://github.com/tardis-sn/tardis/pull/718) Unit test for untested method of montecarlo simulation code (@suyashgupta20) - [#724](https://github.com/tardis-sn/tardis/pull/724) Rebase PR #678 (@yeganer) - [#709](https://github.com/tardis-sn/tardis/pull/709) Add note about broken GUI to docu (@unoebauer) - [#708](https://github.com/tardis-sn/tardis/pull/708) Add new installation instructions (@wkerzendorf) - [#704](https://github.com/tardis-sn/tardis/pull/704) Fix ignoring model tests (@ftsamis) - [#700](https://github.com/tardis-sn/tardis/pull/700) Add contributing guidelines (@wkerzendorf) - [#686](https://github.com/tardis-sn/tardis/pull/686) converted spectrum_frequency (@chinmay0301) - [#696](https://github.com/tardis-sn/tardis/pull/696) Add missing diagnostics property to runner's to_hdf list (@unoebauer) - [#694](https://github.com/tardis-sn/tardis/pull/694) Significantly reduce peak memory usage when vpacket logging is enabled (@ftsamis) - [#682](https://github.com/tardis-sn/tardis/pull/682) Import montecarlo.base in the __init__ module of the package. (@ftsamis) - [#670](https://github.com/tardis-sn/tardis/pull/670) Integrate continuum interactions into cmontecarlo (@chvogl) - [#652](https://github.com/tardis-sn/tardis/pull/652) [TEP006] Aggregate TARDIS restructure and configuration system cleanup (@ftsamis) - [#677](https://github.com/tardis-sn/tardis/pull/677) Update link to tardis_example.yml in documentation - Fix #676 (@unoebauer) - [#674](https://github.com/tardis-sn/tardis/pull/674) Change matplotlib backend - fix test_integration remote plotting issue (@unoebauer) - [#664](https://github.com/tardis-sn/tardis/pull/664) Kd final test (@wkerzendorf, @yeganer) - [#21](https://github.com/tardis-sn/tardis/pull/21) fKd final test (@yeganer) - [#668](https://github.com/tardis-sn/tardis/pull/668) change to tardis atom data on git lfs (@wkerzendorf) - [#666](https://github.com/tardis-sn/tardis/pull/666) Remove News from main TARDIS github page (@unoebauer) - [#667](https://github.com/tardis-sn/tardis/pull/667) Update SOCIS and GSOC students credits (@unoebauer) - [#665](https://github.com/tardis-sn/tardis/pull/665) Add to_hdf compression (@yeganer) - [#663](https://github.com/tardis-sn/tardis/pull/663) Develop (@tardis-sn) - [#657](https://github.com/tardis-sn/tardis/pull/657) Require pyyaml 3.12 (@ftsamis) - [#659](https://github.com/tardis-sn/tardis/pull/659) Update installation docs (@ftsamis) - [#653](https://github.com/tardis-sn/tardis/pull/653) Facility to provide per-setup atom data as well as save report locally. (@karandesai-96) - [#641](https://github.com/tardis-sn/tardis/pull/641) Fix detailed radiative rates (@yeganer) - [#642](https://github.com/tardis-sn/tardis/pull/642) Use pytest-html==1.10.0, modify DokuReport class accordingly. (@karandesai-96) - [#630](https://github.com/tardis-sn/tardis/pull/630) [IntegrationTests] Overview page on Dokuwiki. Running the integration tests will update an overview page on DokuWiki. (@karandesai-96) - [#620](https://github.com/tardis-sn/tardis/pull/620) Runner script to automate execution of integration tests. (@karandesai-96) - [#628](https://github.com/tardis-sn/tardis/pull/628) Remove exponent property from yaml files with exponential density (@ftsamis) - [#626](https://github.com/tardis-sn/tardis/pull/626) Revert "Add exponent as a property for exponential density" (@ftsamis) - [#542](https://github.com/tardis-sn/tardis/pull/542) Updates to He NLTE treatment. (@aoifeboyle) - [#612](https://github.com/tardis-sn/tardis/pull/612) Add facility to generate and accept HDF files as reference data for Integration Tests. (@karandesai-96) - [#614](https://github.com/tardis-sn/tardis/pull/614) Omit the integration_tests when running coveralls (@yeganer) - [#619](https://github.com/tardis-sn/tardis/pull/619) Fixed incorrect name in error message (@Tobychev) - [#618](https://github.com/tardis-sn/tardis/pull/618) to_hdf: If only the last run is stored, do not add a counter in the name (@ftsamis) - [#617](https://github.com/tardis-sn/tardis/pull/617) Add a to_hdf method on TARDISSpectrum (@ftsamis) - [#600](https://github.com/tardis-sn/tardis/pull/600) Parametrize the Slow Test class with two setups. (@karandesai-96) - [#613](https://github.com/tardis-sn/tardis/pull/613) Fix bug in montecarlo.pyx (@yeganer) - [#595](https://github.com/tardis-sn/tardis/pull/595) Line absorption rate estimator (@Tobychev) - [#606](https://github.com/tardis-sn/tardis/pull/606) Merge to_hdf (@ftsamis, @wkerzendorf) - [#585](https://github.com/tardis-sn/tardis/pull/585) [TEP002] Add a to_hdf method to the MontecarloRunner (#585) (@ftsamis) - [#597](https://github.com/tardis-sn/tardis/pull/597) Use abundances, densities filepaths relative to w7 config file. (@karandesai-96) - [#569](https://github.com/tardis-sn/tardis/pull/569) Added a conda environment for tardis (@wkerzendorf) - [#565](https://github.com/tardis-sn/tardis/pull/565) Change the way AtomData quantities are initialized (@yeganer) - [#599](https://github.com/tardis-sn/tardis/pull/599) Update the tardis_example tar file provided in the documentation. (@ftsamis) - [#598](https://github.com/tardis-sn/tardis/pull/598) Fix convergence handling in run_legacy_simulation - fix issue #593 (@unoebauer) - [#590](https://github.com/tardis-sn/tardis/pull/590) Link images of comparison plots in DokuReport using hookwrapper. (@karandesai-96) - [#591](https://github.com/tardis-sn/tardis/pull/591) Fix path of CSS and JS files used in html report. (@karandesai-96) - [#594](https://github.com/tardis-sn/tardis/pull/594) Provide tardis.yaml_load shortcut (@yeganer) - [#592](https://github.com/tardis-sn/tardis/pull/592) Fix virt energy (@yeganer) - [#583](https://github.com/tardis-sn/tardis/pull/583) Subclass pytest-html's HTMLReport to DokuReport class for report generation and upload (@karandesai-96) - [#587](https://github.com/tardis-sn/tardis/pull/587) Move the three spectra attributes from Radial1DModel to MontecarloRunner (@ftsamis) - [#578](https://github.com/tardis-sn/tardis/pull/578) Shift slow test related pytest hooks in lower level conftest.py (#578) (Karan Desai) - [#581](https://github.com/tardis-sn/tardis/pull/581) Update several files to match package_template (@yeganer) - [#576](https://github.com/tardis-sn/tardis/pull/576) [config-system] Validator rewrite: Use jsonschema (@ftsamis) - [#575](https://github.com/tardis-sn/tardis/pull/575) Replace misused calls to yaml.load with a helper function. (@ftsamis) - [#570](https://github.com/tardis-sn/tardis/pull/570) Enable generation of html report of integration tests, and upload to dokuwiki. (@karandesai-96) - [#574](https://github.com/tardis-sn/tardis/pull/574) tardis/base.py: Remove duplicate code from run_tardis (@ftsamis) - [#573](https://github.com/tardis-sn/tardis/pull/573) io/util.py (YAMLLoader): Use OrderedDict to store loaded YAML (@ftsamis) - [#572](https://github.com/tardis-sn/tardis/pull/572) Change the way YAMLLoader resolves some properties (@ftsamis) - [#532](https://github.com/tardis-sn/tardis/pull/532) Documentation overhaul (@unoebauer, @chvogl) - [#571](https://github.com/tardis-sn/tardis/pull/571) data/tardis_config_definition.yml: Set the exponent property as mandatory when density is exponential. (#571) (@ftsamis) - [#566](https://github.com/tardis-sn/tardis/pull/566) Initial laydown of comparison plots for TestW7. (#566) (Karan Desai) - [#567](https://github.com/tardis-sn/tardis/pull/567) Accept keyword arguments for Configuration.from_yaml (@yeganer) - [#561](https://github.com/tardis-sn/tardis/pull/561) TestW7: Assertions for spectrum quantities, fixture for handling baseline data. (@karandesai-96) - [#515](https://github.com/tardis-sn/tardis/pull/515) [config-system] Add a custom YAML Loader to parse astropy quantities (@ftsamis) - [#555](https://github.com/tardis-sn/tardis/pull/555) Use pytest's monkeypatch.chdir to change the working directory in the config_reader tests (@ftsamis, @lukeshingles) - [#558](https://github.com/tardis-sn/tardis/pull/558) Integration Test class for Stratified W7 setup. (@karandesai-96) - [#557](https://github.com/tardis-sn/tardis/pull/557) Enable skipping slow tests. (@karandesai-96) - [#544](https://github.com/tardis-sn/tardis/pull/544) Continue cmontecarlo tests refactor. Extend #530. (@karandesai-96) - [#543](https://github.com/tardis-sn/tardis/pull/543) Fix issue #535: Treat rel. paths inside config relative to the config file (@lukeshingles, @ftsamis) - [#1](https://github.com/tardis-sn/tardis/pull/1) Write tests for the issue #535 fix. (@ftsamis) - [#551](https://github.com/tardis-sn/tardis/pull/551) Add SOCIS 2016 advertisement (@unoebauer) - [#547](https://github.com/tardis-sn/tardis/pull/547) Fix Issue #548 (@karandesai-96) - [#545](https://github.com/tardis-sn/tardis/pull/545) added mailmap to compile the commits for each person (#545) (@wkerzendorf) - [#539](https://github.com/tardis-sn/tardis/pull/539) Adding OSX to our travis build (#539) (@wkerzendorf) - [#541](https://github.com/tardis-sn/tardis/pull/541) Move progress bar update after calculation (#541) (@yeganer) - [#540](https://github.com/tardis-sn/tardis/pull/540) Mirroring C enums in Python for CMontecarlo tests. (@karandesai-96) - [#538](https://github.com/tardis-sn/tardis/pull/538) Upgrading to the new Readthedocs infrastructure (#538) (@wkerzendorf) - [#530](https://github.com/tardis-sn/tardis/pull/530) Refactor cmontecarlo testing framework (@karandesai-96) - [#537](https://github.com/tardis-sn/tardis/pull/537) Ignore invalid OpenMP nthreads values (#537) (@yeganer) - [#533](https://github.com/tardis-sn/tardis/pull/533) Remove rpacket.recently_crossed_boundary flag (@yeganer) - [#514](https://github.com/tardis-sn/tardis/pull/514) Performance (@yeganer) - [#531](https://github.com/tardis-sn/tardis/pull/531) Organize headers in C-Extension (@yeganer) - [#526](https://github.com/tardis-sn/tardis/pull/526) Docs: Include conda-requirements in installation.rst (@karandesai-96) - [#519](https://github.com/tardis-sn/tardis/pull/519) Documentation:Installation modify command (@yeganer) - [#510](https://github.com/tardis-sn/tardis/pull/510) Updates requirements to solve libgfortran error. Fixes #509 (@karandesai-96) - [#495](https://github.com/tardis-sn/tardis/pull/495) Fix energy conservation (@unoebauer) - [#486](https://github.com/tardis-sn/tardis/pull/486) Bugfix radiative rates type detailed (@chvogl, @unoebauer) - [#488](https://github.com/tardis-sn/tardis/pull/488) Fix indentation in c extension (@yeganer) - [#494](https://github.com/tardis-sn/tardis/pull/494) Fix #493 (@yeganer) - [#1](https://github.com/tardis-sn/tardis/pull/1) Add simple test for j_blue_estimator (@unoebauer) - [#491](https://github.com/tardis-sn/tardis/pull/491) Include IDE specific auto-generated files in .gitignore. Fixes #490 (@karandesai-96) - [#485](https://github.com/tardis-sn/tardis/pull/485) Montecarlo progress (@yeganer) - [#457](https://github.com/tardis-sn/tardis/pull/457) Fix Issue #454 (@yeganer) - [#484](https://github.com/tardis-sn/tardis/pull/484) Minor improvement of vpacket logging scheme (@unoebauer) - [#479](https://github.com/tardis-sn/tardis/pull/479) added units to test_simulation.py (@mishinma) - [#469](https://github.com/tardis-sn/tardis/pull/469) Changed the Link for AstroPy's dev workflow (@souravsingh) - [#481](https://github.com/tardis-sn/tardis/pull/481) Introcuding safe_malloc and safe_realloc macros: fixes #480 (@unoebauer) - [#475](https://github.com/tardis-sn/tardis/pull/475) Reorganize import statements in atomic.py (@Pratik151) - [#471](https://github.com/tardis-sn/tardis/pull/471) Quickfix to solve Issue #455 and #464 (@yeganer) - [#472](https://github.com/tardis-sn/tardis/pull/472) fixed build of documentation on readthedocs (@wkerzendorf) - [#461](https://github.com/tardis-sn/tardis/pull/461) Bugfix test cmontecarlo (@yeganer) - [#452](https://github.com/tardis-sn/tardis/pull/452) Build fix and nthreads fix - fixes #356 (@unoebauer) - [#450](https://github.com/tardis-sn/tardis/pull/450) Checking for zero-volume cells: Fixes issue #79 (@unoebauer) - [#449](https://github.com/tardis-sn/tardis/pull/449) added test to verify virtual spectrum (@unoebauer) - [#446](https://github.com/tardis-sn/tardis/pull/446) calculate virtual spectrum independently of vpacket loggin - fixes #445 (@unoebauer) - [#440](https://github.com/tardis-sn/tardis/pull/440) started addressing issue #436 (@unoebauer) - [#426](https://github.com/tardis-sn/tardis/pull/426) Simulation - restructure (@wkerzendorf) - [#434](https://github.com/tardis-sn/tardis/pull/434) updated the .travis.yml file to do a rehash before executing conda (@wkerzendorf) - [#433](https://github.com/tardis-sn/tardis/pull/433) Optional vpacket logging WIP (@tardis-sn) - [#425](https://github.com/tardis-sn/tardis/pull/425) Updated nlte.rst (@souravsingh) - [#424](https://github.com/tardis-sn/tardis/pull/424) added a new requirement for astropy (@wkerzendorf) - [#1](https://github.com/tardis-sn/tardis/pull/1) Update nlte.rst (@souravsingh) - [#375](https://github.com/tardis-sn/tardis/pull/375) made sure that atomic does not reinsert the index into the dataframe (@wkerzendorf) - [#420](https://github.com/tardis-sn/tardis/pull/420) Memory issue (@wkerzendorf) - [#416](https://github.com/tardis-sn/tardis/pull/416) added new version requirements for pandas and astropy (@wkerzendorf) - [#414](https://github.com/tardis-sn/tardis/pull/414) Improvements to He approximation. (@aoifeboyle) - [#413](https://github.com/tardis-sn/tardis/pull/413) WIP Docstrings (@wkerzendorf) - [#412](https://github.com/tardis-sn/tardis/pull/412) Fix for zeta issues. (@wkerzendorf) - [#3](https://github.com/tardis-sn/tardis/pull/3) Plasma/ab zeta fix (@wkerzendorf) - [#410](https://github.com/tardis-sn/tardis/pull/410) WIP: Cleaning up plasma (@wkerzendorf) - [#399](https://github.com/tardis-sn/tardis/pull/399) Plasma optimization (@wkerzendorf, @mreineck) - [#2](https://github.com/tardis-sn/tardis/pull/2) fix for chi_0 problem (@wkerzendorf) - [#19](https://github.com/tardis-sn/tardis/pull/19) Plasma optimisation fix. (@aoifeboyle) - [#404](https://github.com/tardis-sn/tardis/pull/404) Montecarlo/new packet source (@wkerzendorf) - [#407](https://github.com/tardis-sn/tardis/pull/407) Organising of plasma base files. (@aoifeboyle) - [#405](https://github.com/tardis-sn/tardis/pull/405) Pandas macroatom issue fix (@wkerzendorf) - [#406](https://github.com/tardis-sn/tardis/pull/406) Numerical He NLTE. (@aoifeboyle) - [#401](https://github.com/tardis-sn/tardis/pull/401) Alternative fix for issue #393 (@mreineck) - [#398](https://github.com/tardis-sn/tardis/pull/398) More cleanups (@mreineck) - [#400](https://github.com/tardis-sn/tardis/pull/400) Change to NLTE properties (@aoifeboyle) - [#397](https://github.com/tardis-sn/tardis/pull/397) Montecarlo/memoryview (@wkerzendorf) - [#396](https://github.com/tardis-sn/tardis/pull/396) added virt_packet properties to to_hdf5 list (Kromer plot) (@unoebauer) - [#391](https://github.com/tardis-sn/tardis/pull/391) More work on cmontecarlo.c and the unit tests (@mreineck) - [#364](https://github.com/tardis-sn/tardis/pull/364) added tardis stats (@wkerzendorf) - [#392](https://github.com/tardis-sn/tardis/pull/392) Consistency between old virtual packet arrays and new ones introduced in PR 384 (@unoebauer) - [#389](https://github.com/tardis-sn/tardis/pull/389) changes to address issue #388 (@mreineck) - [#386](https://github.com/tardis-sn/tardis/pull/386) improve inlining specifications and fix a few problems (@mreineck) - [#384](https://github.com/tardis-sn/tardis/pull/384) Minor changes in Monte Carlo and model part for Kromer plots (@unoebauer) - [#374](https://github.com/tardis-sn/tardis/pull/374) WIP: Helium approx. (@wkerzendorf) - [#382](https://github.com/tardis-sn/tardis/pull/382) Improvements to plasma graph (@aoifeboyle) - [#381](https://github.com/tardis-sn/tardis/pull/381) Fix to plasma issue with GUI. (@aoifeboyle) - [#379](https://github.com/tardis-sn/tardis/pull/379) Fix of to_hdf5. (@aoifeboyle) - [#377](https://github.com/tardis-sn/tardis/pull/377) Plasma static methods (@aoifeboyle) - [#373](https://github.com/tardis-sn/tardis/pull/373) Removing test_plasma_nlte.py. (@aoifeboyle) - [#372](https://github.com/tardis-sn/tardis/pull/372) Correcting some old plasma tests. (@aoifeboyle) - [#304](https://github.com/tardis-sn/tardis/pull/304) Plasma restructure (@wkerzendorf) - [#370](https://github.com/tardis-sn/tardis/pull/370) Removed some tests temporarily. (@aoifeboyle) - [#369](https://github.com/tardis-sn/tardis/pull/369) Removed import plasma_array (@aoifeboyle) - [#368](https://github.com/tardis-sn/tardis/pull/368) Fixing plasma merge (@aoifeboyle) - [#367](https://github.com/tardis-sn/tardis/pull/367) preparing for the new container archictecture used by travis (@wkerzendorf) - [#365](https://github.com/tardis-sn/tardis/pull/365) LTE Plasma Test (@aoifeboyle) - [#361](https://github.com/tardis-sn/tardis/pull/361) Added formulae to graph. (@aoifeboyle) - [#360](https://github.com/tardis-sn/tardis/pull/360) Rebasedvirtrunner (@orbitfold, @wkerzendorf) - [#362](https://github.com/tardis-sn/tardis/pull/362) Adjusted stimulated emission factor for NLTE. (@aoifeboyle) - [#355](https://github.com/tardis-sn/tardis/pull/355) Add with-openmp to develop (@orbitfold) - [#354](https://github.com/tardis-sn/tardis/pull/354) added print statement for openmp (@wkerzendorf) - [#350](https://github.com/tardis-sn/tardis/pull/350) Tidying/Testing/Documenting Plasma (@aoifeboyle) - [#352](https://github.com/tardis-sn/tardis/pull/352) Attempt at solution. (@aoifeboyle) - [#330](https://github.com/tardis-sn/tardis/pull/330) [GSoC 2015 WIP] Testing other montecarlo functions (@kaushik94) - [#347](https://github.com/tardis-sn/tardis/pull/347) NLTE (@aoifeboyle) - [#325](https://github.com/tardis-sn/tardis/pull/325) Bound-free interactions (@chvogl) - [#344](https://github.com/tardis-sn/tardis/pull/344) Plasma/multiple outputs (@aoifeboyle) - [#346](https://github.com/tardis-sn/tardis/pull/346) linked the plasma documentation again (@wkerzendorf) - [#338](https://github.com/tardis-sn/tardis/pull/338) OpenMP WIP (@orbitfold) - [#343](https://github.com/tardis-sn/tardis/pull/343) Plasma/multi output (@wkerzendorf) - [#17](https://github.com/tardis-sn/tardis/pull/17) Fixes. (@aoifeboyle) - [#324](https://github.com/tardis-sn/tardis/pull/324) Gui package (WIP) (@gautam1168) - [#327](https://github.com/tardis-sn/tardis/pull/327) [GSoC 2015 MRG] Testing getters setters (@kaushik94) - [#322](https://github.com/tardis-sn/tardis/pull/322) Updating the gui documentation. (@gautam1168) - [#296](https://github.com/tardis-sn/tardis/pull/296) Gui with menubars(WIP) (@gautam1168) - [#320](https://github.com/tardis-sn/tardis/pull/320) virtual packets frequency cut (@unoebauer) - [#314](https://github.com/tardis-sn/tardis/pull/314) Installation FAQ (@wkerzendorf) - [#310](https://github.com/tardis-sn/tardis/pull/310) A more detailed description of the montecarlo process (@wkerzendorf) - [#301](https://github.com/tardis-sn/tardis/pull/301) [GSoC 2015 MRG] Restructuring Montecarlo (@kaushik94) - [#234](https://github.com/tardis-sn/tardis/pull/234) Removing usage of yield in test_utils.py (@kaushik94) - [#299](https://github.com/tardis-sn/tardis/pull/299) Test of model_reader.py (@wkerzendorf, @ssim) - [#288](https://github.com/tardis-sn/tardis/pull/288) -fixed discrepancy concerning hold_iterations (@unoebauer) - [#286](https://github.com/tardis-sn/tardis/pull/286) Proposal for a new to HD5 function. (@mklauser) - [#283](https://github.com/tardis-sn/tardis/pull/283) fixed the reader for the older Paper1 format yaml files (@wkerzendorf) - [#269](https://github.com/tardis-sn/tardis/pull/269) Miscellaneous README changes (@iKevinY) - [#251](https://github.com/tardis-sn/tardis/pull/251) gui.py and running.rst edited for PyQt4 and PySide (@gautam1168) - [#250](https://github.com/tardis-sn/tardis/pull/250) Docs/pip reqs (@wkerzendorf) - [#244](https://github.com/tardis-sn/tardis/pull/244) added coverage back (@wkerzendorf) - [#240](https://github.com/tardis-sn/tardis/pull/240) rename of pip-requirements to conda-requirements (@wkerzendorf) - [#225](https://github.com/tardis-sn/tardis/pull/225) Test added in test_atomic.py (@vaibhav4595) - [#223](https://github.com/tardis-sn/tardis/pull/223) Update git_workflow.rst (@ujjwalwahi) ### 1.0rc3 (2015/03/03 12:54 +00:00) - [#219](https://github.com/tardis-sn/tardis/pull/219) fixing run_tardis (@wkerzendorf) ### 1.0.dev1419 (2015/02/19 13:58 +00:00) - [#218](https://github.com/tardis-sn/tardis/pull/218) Docs/anaconda install (@wkerzendorf) - [#217](https://github.com/tardis-sn/tardis/pull/217) Docs/fixing pip requirements (@wkerzendorf) - [#216](https://github.com/tardis-sn/tardis/pull/216) some fixes to the gui so it works with pyside (@wkerzendorf) - [#214](https://github.com/tardis-sn/tardis/pull/214) Preparing the docs for V1 (@wkerzendorf) - [#210](https://github.com/tardis-sn/tardis/pull/210) a restructure of the C-file file structure (@wkerzendorf, @mklauser) - [#7](https://github.com/tardis-sn/tardis/pull/7) include .c in montecarlo/src/ for the randomkit files (@mklauser) - [#209](https://github.com/tardis-sn/tardis/pull/209) Testing/pandas version info (@wkerzendorf) - [#205](https://github.com/tardis-sn/tardis/pull/205) As simpler `run_tardis` (@wkerzendorf) - [#206](https://github.com/tardis-sn/tardis/pull/206) Minor but critical fix to binary search (reverse) (@ssim) - [#199](https://github.com/tardis-sn/tardis/pull/199) Gnuify cmontecarlo.c and cmontecarlo.h files (@orbitfold) - [#203](https://github.com/tardis-sn/tardis/pull/203) Docs/reporting bugs (@wkerzendorf) - [#201](https://github.com/tardis-sn/tardis/pull/201) A critical warning was added to the model indicating that no packet has left the simulation through the outer boundary. (@mklauser) - [#200](https://github.com/tardis-sn/tardis/pull/200) added a new location for the atomic data. (@wkerzendorf) - [#196](https://github.com/tardis-sn/tardis/pull/196) New binary search added (@mklauser) - [#169](https://github.com/tardis-sn/tardis/pull/169) fix for #168 (@mklauser) - [#194](https://github.com/tardis-sn/tardis/pull/194) Setup/fix requirements (@wkerzendorf) - [#188](https://github.com/tardis-sn/tardis/pull/188) A macro to automagically fix inline issues (@orbitfold) - [#190](https://github.com/tardis-sn/tardis/pull/190) General/fixing unit problems (@wkerzendorf) - [#183](https://github.com/tardis-sn/tardis/pull/183) Added colon (@sofiatti) - [#179](https://github.com/tardis-sn/tardis/pull/179) making sure that if last_no_of_packets is not specified that it is set t... (@wkerzendorf) - [#178](https://github.com/tardis-sn/tardis/pull/178) Atomic/fix reprepare (@wkerzendorf) - [#177](https://github.com/tardis-sn/tardis/pull/177) added from_yaml and from_config_dict to ConfigurationNameSpace (@wkerzendorf) - [#175](https://github.com/tardis-sn/tardis/pull/175) Fix a few problems in cmontecarlo.c (@orbitfold, @wkerzendorf) - [#174](https://github.com/tardis-sn/tardis/pull/174) fixes added for clang compile on mac (@wkerzendorf) - [#171](https://github.com/tardis-sn/tardis/pull/171) Fix issues when using clang compiler (issue #170) (@orbitfold) - [#167](https://github.com/tardis-sn/tardis/pull/167) fix for #165 (@mklauser, @wkerzendorf) - [#3](https://github.com/tardis-sn/tardis/pull/3) testing the new t_inner fix (@wkerzendorf) - [#164](https://github.com/tardis-sn/tardis/pull/164) Config/toggle validation (@wkerzendorf) - [#151](https://github.com/tardis-sn/tardis/pull/151) WIP Montecarlo C Rewrite (@orbitfold) - [#160](https://github.com/tardis-sn/tardis/pull/160) how to get constant density? broken? (@wkerzendorf) ### 0.9.2 (2014/06/12 23:37 +00:00) - [#158](https://github.com/tardis-sn/tardis/pull/158) updated astropy_helpers version (@wkerzendorf) - [#157](https://github.com/tardis-sn/tardis/pull/157) added yaml to pip-requirements and linked the doc pip-requirements to this (@wkerzendorf) - [#154](https://github.com/tardis-sn/tardis/pull/154) renamed Config to ConfigurationValidator (@wkerzendorf) - [#153](https://github.com/tardis-sn/tardis/pull/153) General mixup of 0.9.2b1 (@wkerzendorf) - [#152](https://github.com/tardis-sn/tardis/pull/152) importing problems with new C functions? (@wkerzendorf) - [#149](https://github.com/tardis-sn/tardis/pull/149) Edits to docs (@ssim) - [#150](https://github.com/tardis-sn/tardis/pull/150) Montecarlo flowchart (@orbitfold) - [#148](https://github.com/tardis-sn/tardis/pull/148) fixed config_validator log_lsun check (@wkerzendorf) - [#142](https://github.com/tardis-sn/tardis/pull/142) WIP Porting utility functions to C (issue #131) (@orbitfold) - [#137](https://github.com/tardis-sn/tardis/pull/137) TRAVIS passes. (@wkerzendorf) - [#143](https://github.com/tardis-sn/tardis/pull/143) Updating configuration name space (@wkerzendorf) - [#136](https://github.com/tardis-sn/tardis/pull/136) Updating the config reader to work with the validator (@wkerzendorf, @mklauser) - [#145](https://github.com/tardis-sn/tardis/pull/145) Adding full spectrum generation test to TRAVIS (@wkerzendorf) - [#144](https://github.com/tardis-sn/tardis/pull/144) Setup/switch to astropy helpers (@wkerzendorf) - [#6](https://github.com/tardis-sn/tardis/pull/6) Pr136 (@mklauser) - [#5](https://github.com/tardis-sn/tardis/pull/5) Pr136 (@mklauser) - [#4](https://github.com/tardis-sn/tardis/pull/4) Pr136 (@mklauser) - [#3](https://github.com/tardis-sn/tardis/pull/3) Pr136 (@mklauser) - [#2](https://github.com/tardis-sn/tardis/pull/2) bug fix for the container handling. ToDo Remove remove general except in... (@mklauser) - [#135](https://github.com/tardis-sn/tardis/pull/135) Adding documentation for d_inner and d_outer calculation (@wkerzendorf) - [#132](https://github.com/tardis-sn/tardis/pull/132) i try to rebase the dp to the master (@mklauser) - [#134](https://github.com/tardis-sn/tardis/pull/134) Test high temperature - outside of interpolation range of zeta factor (@wkerzendorf) - [#129](https://github.com/tardis-sn/tardis/pull/129) Re-implement binary_search in C (@orbitfold) - [#127](https://github.com/tardis-sn/tardis/pull/127) Docs edit only ("accessing physical quantities") (@ssim) - [#116](https://github.com/tardis-sn/tardis/pull/116) Adding documentation for Workflow (@wkerzendorf, @ssim) - [#112](https://github.com/tardis-sn/tardis/pull/112) NLTE fixes - discussion needed before merge - relates to #109 (@ssim, @wkerzendorf) - [#11](https://github.com/tardis-sn/tardis/pull/11) fixing up the NLTE tests (@wkerzendorf) - [#10](https://github.com/tardis-sn/tardis/pull/10) Plasma/fix nlte tests (@wkerzendorf) - [#122](https://github.com/tardis-sn/tardis/pull/122) proposed restructing of binary search/line search (@ssim, @wkerzendorf, @mklauser) - [#9](https://github.com/tardis-sn/tardis/pull/9) Issue 123two (@mklauser) - [#124](https://github.com/tardis-sn/tardis/pull/124) updated current_public_table.rst (@wkerzendorf) - [#7](https://github.com/tardis-sn/tardis/pull/7) Fix line search (@wkerzendorf) - [#6](https://github.com/tardis-sn/tardis/pull/6) updated documentation to numpydoc standard (@wkerzendorf) - [#121](https://github.com/tardis-sn/tardis/pull/121) warning added for density file readin outside tabulated range (@ssim) - [#119](https://github.com/tardis-sn/tardis/pull/119) Fix to deal with possible problem in end of line list (@ssim) - [#118](https://github.com/tardis-sn/tardis/pull/118) Fix for the issue #84 Pull request for fixes / documentation edits related to the profiles (@ssim, @mklauser) - [#91](https://github.com/tardis-sn/tardis/pull/91) Documentation update to download atomic databases (@wkerzendorf) - [#110](https://github.com/tardis-sn/tardis/pull/110) #106 suggestion for private variable names (@mklauser, @ssim) - [#111](https://github.com/tardis-sn/tardis/pull/111) minor fixed / logger statements (@ssim) - [#97](https://github.com/tardis-sn/tardis/pull/97) Fix for issue #81: Add warning if w > 1. (@thegyro) - [#92](https://github.com/tardis-sn/tardis/pull/92) Adding a simple test to run a full calculation (@wkerzendorf) - [#101](https://github.com/tardis-sn/tardis/pull/101) Fix for Issue #88: Moved test functions for tardis.util from test_config_reader (@thegyro) - [#94](https://github.com/tardis-sn/tardis/pull/94) Fix coveralls (@wkerzendorf) - [#87](https://github.com/tardis-sn/tardis/pull/87) Added --profile and --profiler_log_file command line arguments to enable... (@orbitfold) ### 0.9.1 (2014/02/04 01:51 +00:00) - [#74](https://github.com/tardis-sn/tardis/pull/74) fixed manifest to incluse ez_setup.py and setuptools_bootstrap.py. fixes... (@wkerzendorf) - [#78](https://github.com/tardis-sn/tardis/pull/78) cosmetic fixes (@ssim) - [#77](https://github.com/tardis-sn/tardis/pull/77) Docs edit (@ssim, @wkerzendorf) - [#1](https://github.com/tardis-sn/tardis/pull/1) Docs fix (@wkerzendorf, @ssim) - [#76](https://github.com/tardis-sn/tardis/pull/76) stuff with abundance profile readin (@ssim) - [#75](https://github.com/tardis-sn/tardis/pull/75) work on gui fixing (@ssim) - [#72](https://github.com/tardis-sn/tardis/pull/72) documentation update for release (@wkerzendorf) - [#71](https://github.com/tardis-sn/tardis/pull/71) New configuration style (@wkerzendorf) - [#70](https://github.com/tardis-sn/tardis/pull/70) added simple coveralls.io in there (@wkerzendorf) - [#69](https://github.com/tardis-sn/tardis/pull/69) Atomic/atomic symbols (@wkerzendorf) - [#67](https://github.com/tardis-sn/tardis/pull/67) Config/ascii file reader (@wkerzendorf) - [#68](https://github.com/tardis-sn/tardis/pull/68) Tests/fixing2 (@wkerzendorf) - [#61](https://github.com/tardis-sn/tardis/pull/61) gui fix (@ssim) - [#60](https://github.com/tardis-sn/tardis/pull/60) General bugfixing (@wkerzendorf) - [#59](https://github.com/tardis-sn/tardis/pull/59) General bugfixing (@wkerzendorf, @nathanielatom, @ssim, @maryampatel) - [#54](https://github.com/tardis-sn/tardis/pull/54) Montecarlo/reflection (@ssim) - [#52](https://github.com/tardis-sn/tardis/pull/52) Montecarlo/reflection (@ssim, @wkerzendorf, @maryampatel, @nathanielatom) - [#51](https://github.com/tardis-sn/tardis/pull/51) Model/optimizig (@nathanielatom) - [#50](https://github.com/tardis-sn/tardis/pull/50) Gui/span (@nathanielatom) - [#49](https://github.com/tardis-sn/tardis/pull/49) Gui/span (@nathanielatom) - [#48](https://github.com/tardis-sn/tardis/pull/48) Gui/span (@nathanielatom, @wkerzendorf, @maryampatel) - [#39](https://github.com/tardis-sn/tardis/pull/39) General bugfixing (@wkerzendorf, @nathanielatom, @maryampatel) - [#46](https://github.com/tardis-sn/tardis/pull/46) Gui/dialogue (@nathanielatom, @wkerzendorf) - [#41](https://github.com/tardis-sn/tardis/pull/41) Gui/docs (@nathanielatom) - [#40](https://github.com/tardis-sn/tardis/pull/40) Gui/matplotlib figure (@nathanielatom, @maryampatel) - [#34](https://github.com/tardis-sn/tardis/pull/34) General bugfixing (@wkerzendorf) - [#32](https://github.com/tardis-sn/tardis/pull/32) Plasma/testing2 (@maryampatel) - [#29](https://github.com/tardis-sn/tardis/pull/29) General bugfixing looks good to me (@wkerzendorf) - [#28](https://github.com/tardis-sn/tardis/pull/28) The same as last time but with small changes. (@mklauser) - [#26](https://github.com/tardis-sn/tardis/pull/26) Plasma/bound free (@mklauser) - [#25](https://github.com/tardis-sn/tardis/pull/25) Simulation/run single simulation (@wkerzendorf) ### v0.9a (2013/02/14 21:15 +00:00) - [#24](https://github.com/tardis-sn/tardis/pull/24) Montecarlo/extract - seems fine merging (@ssim) - [#22](https://github.com/tardis-sn/tardis/pull/22) Montecarlo/fix convergence (@wkerzendorf, @ssim) - [#20](https://github.com/tardis-sn/tardis/pull/20) Plasma/testing (@maryampatel) - [#18](https://github.com/tardis-sn/tardis/pull/18) Docs/fixdocs (@maryampatel) - [#17](https://github.com/tardis-sn/tardis/pull/17) Docs/fixdocs (@maryampatel) - [#16](https://github.com/tardis-sn/tardis/pull/16) Doc/atomic preliminary merge (@maryampatel) - [#14](https://github.com/tardis-sn/tardis/pull/14) Implemented all changes (@maryampatel) - [#13](https://github.com/tardis-sn/tardis/pull/13) Changed the main documentation page (@maryampatel)