scipion-em-xmipp 25.6.1__py3-none-any.whl → 26.0.0__py3-none-any.whl

{scipion_em_xmipp-25.6.1.dist-info → scipion_em_xmipp-26.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: scipion-em-xmipp
-Version: 25.6.1
+Version: 26.0.0
 Summary: Plugin to use Xmipp programs within the Scipion framework.
 Author-email: Oier Lauzirika Zarrabeitia <oierlauzi@bizkaia.eu>, Alberto Garcia Mena <alberto.garcia@cnb.csic.es>, Carlos Oscar Sanchez Sorzano <coss@cnb.csic.es>
 License: GNU General Public License v3 (GPLv3)
@@ -20,6 +20,9 @@ Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
 Requires-Dist: PyWavelets
+Requires-Dist: xmipp3-installer==2.*
+Requires-Dist: numpy==1.*
+Dynamic: license-file
 
 [![Build](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml/badge.svg)](https://github.com/I2PC/scipion-em-xmipp/actions/workflows/build.yml)
 

{scipion_em_xmipp-25.6.1.dist-info → scipion_em_xmipp-26.0.0.dist-info}/RECORD

@@ -1,12 +1,15 @@
-xmipp3/__init__.py,sha256=x1aoX3RaunI-nRMtGoSP_PFb_UmJIFFTxtYbSD4ulRM,13179
+scipion_em_xmipp-26.0.0.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+xmipp3/__init__.py,sha256=4PeNbua-W_1eZBVeFmS5_iID8P0s97UJKSWEVKCnPks,13251
 xmipp3/base.py,sha256=ehZ6iRN1EpZHU_XTmonvoFpDf7xY_1tfPOHDB90KgCk,21294
 xmipp3/bibtex.py,sha256=YZjuuB_9RC4QOOy5r86cRX3ze2EWz43iGzIDQvtu5HQ,28310
 xmipp3/checkProtocolsConf.py,sha256=eJhADp1lv3Mdwe5yYdsVJcVzjelUCqoLHs43XSGzrDo,4428
-xmipp3/constants.py,sha256=SjO3ViST8YrLIn49QqymQNrNwzM1wzG9VOupvnyM-_U,3953
+xmipp3/constants.py,sha256=r24zKoKNKhc0rj0UWD6KrF18PAdBheX9fwKGobd-Y7Q,3954
+xmipp3/logParser.py,sha256=qiBJNqNxSP7o_6yDJkVgJV2OlzK0vMfpErzc2qCZ6Lo,2229
 xmipp3/programs.py,sha256=yrMD0EHEq5j_ODCeINbaCp4CEqSgkmioan1O1mAgPY0,11968
 xmipp3/protocols.conf,sha256=rqtLT-tHUh2L8AyQl3BAk5A926MyRwVEVAKprvByiEQ,14988
+xmipp3/protocolsCollectInfo.py,sha256=Y36i4yDjhcjzQvBAvB00rGhoRl3gxU2Vy8K_ZgSHl04,10059
 xmipp3/utils.py,sha256=JKuEdR40rn6pdm0puwsgzItbNnrFL4sa7pBymVtRzLM,9125
-xmipp3/version.py,sha256=3xcOfVaQaeACLrBm9CF1PrOSgSL9GYkCXs4oZUH9OTw,1803
+xmipp3/version.py,sha256=75E4bkjhIA86kcNnpjapd2PaMptMj2rjr89LYoSvNN8,2101
 xmipp3/wizards.py,sha256=IgT3uCiOYBLOkhX7GWdKcwHOPyZD783HQG0jSjdovRk,20452
 xmipp3/xmipp_logo.png,sha256=ggrFNUy5UEBjvKfNvu0T14Kzolnhc-ij9AQ734R27MY,84496
 xmipp3/xmipp_logo_devel.png,sha256=IQI1XWogTHbJ5UClpatiNcZfwZB7U3zWG3oThpXOvmc,749745
@@ -14,6 +17,8 @@ xmipp3/convert/__init__.py,sha256=y231wRpfDySMgyjLi6xYuO3hTG1NZBNnMRT7dNnYqu8,12
 xmipp3/convert/convert.py,sha256=fcFljt804tFRjAWPWaGNktq5oz1jpdLOV3R59odhGCs,63249
 xmipp3/convert/dataimport.py,sha256=ssmMLKU1qXDuqjStNJv-zfYNJAJ-0k7EzNyF4jf91IU,13292
 xmipp3/convert/io_coordinates.py,sha256=ZUKEbL7DjJ0jDVJzs2Nnc-sX7QYuAyGSponhP6WYMDI,1963
+xmipp3/legacy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xmipp3/legacy/protocols/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 xmipp3/legacy/protocols/protocol_angular_resolution_alignment.py,sha256=EsKm1PfGkkpnzoKuhZqM-e1_99_XVtIBOIGhlgg45qM,8521
 xmipp3/legacy/protocols/protocol_apply_deformation_zernike3d.py,sha256=rlRxaTNmp8X0WBNwBZNF_QTCS38WnUzBtg1M25_aNOo,5673
 xmipp3/legacy/protocols/protocol_classification_gpuCorr.py,sha256=oiyTNfVp5GNgQD8hJsUl93N_jiEEvTdWAPhIYWBNKhE,37013
@@ -23,6 +28,7 @@ xmipp3/legacy/protocols/protocol_classify_kmeans2d.py,sha256=6yZz3o2dooZmo-83vHc
 xmipp3/legacy/protocols/protocol_deep_align.py,sha256=61Ju9mgKLB9Sk07KkwH3D932xP137kVsA-ca_9lnDHM,37232
 xmipp3/legacy/protocols/protocol_deep_denoising.py,sha256=z7lkqP8AylC1NMbHkGORUKLAiS9DAffInaZUpbYAAVo,21324
 xmipp3/legacy/protocols/protocol_enrich.py,sha256=pymPJpNAHUNtECe89-pdzcVmkdNbVN7kp1PGz9NgwYg,25080
+xmipp3/legacy/protocols/protocol_extract_particles_movies.py,sha256=uq5NtTvqe-ewFjIAaD3lN2RTaaPUgPbfjAiqnpwl13s,23298
 xmipp3/legacy/protocols/protocol_kmeans_clustering.py,sha256=VKQ3IRRvKMozBSSWb8dRBmoeGbsKjYgqZmuez1XAEWA,5664
 xmipp3/legacy/protocols/protocol_metaprotocol_create_output.py,sha256=-f_-TQodTDufYkhVzQCt8d4h55fKdRjUJzHvSH7s4Ns,6121
 xmipp3/legacy/protocols/protocol_metaprotocol_create_subset.py,sha256=Z1dg0H88x00b2W47Ta7qASbDND-zXyDKQnZ2dN2UPw4,3915
@@ -49,16 +55,16 @@ xmipp3/legacy/tests/test_protocols_metaprotocol_heterogeneity.py,sha256=JWVKPp88
 xmipp3/legacy/tests/test_protocols_mixed_movies.py,sha256=4ao-hu9kk4B8LWwWVJedGcpFfzysb2p6Gr8mgP2DoD4,6225
 xmipp3/legacy/tests/test_protocols_solid_angles.py,sha256=vJ5hrZqRYfPrp9bP9SYLDqzVO__kL6AjAOBJOeajJR0,6985
 xmipp3/legacy/tests/test_protocols_subtract_projection.py,sha256=eJXuL_Z5CYVdSg5jX_wC2_xZWdt66HclGyzo9NQGVSc,46216
-xmipp3/legacy/tests/test_protocols_xmipp_movies.py,sha256=8cQ_OJoUjzlEKcDuXHmyoMXLa60DI_5S_psoGtRdxkA,9610
+xmipp3/legacy/tests/test_protocols_xmipp_movies.py,sha256=LCcxGEUeixG1_qJpsCAAZYutmE3L30I8YonVmV3sFOY,15031
 xmipp3/legacy/viewers/viewer_angular_resolution_alignment.py,sha256=9DCZ94TAedHltvlKf99BEFtgFuoMisKipMwubPn82lU,5155
 xmipp3/legacy/viewers/viewer_deep_align.py,sha256=yCYVQq28r1pGbe4Ss_s5Ki65NTbkL71RUb78ny1EHuo,5621
 xmipp3/legacy/viewers/viewer_metaprotocol_golden_highres.py,sha256=PwfPMwTo4z_4Fzc-fBV7VLf4RswvMwoF9vlAqd1o9uI,5373
 xmipp3/legacy/viewers/viewer_mltomo.py,sha256=IjSnHQqkZCG45C6B560HV7flW1OGUr2OugGuECs_Zsk,12178
 xmipp3/legacy/viewers/viewer_solid_angles.py,sha256=S2QANz-8VdoK_8kKTYtkhI6SkPQyRuiPkMaz2bQJCIY,3970
 xmipp3/legacy/viewers/viewer_split_volume.py,sha256=4rmH0ixpNS1eR_FLgmD5lgo4IUmqTPNST7_-wLMHkj4,2146
-xmipp3/protocols/__init__.py,sha256=G_LBrSRvKGK4aVXMWY1P3hC3mwBWiAU-JmeI_31yE04,8359
-xmipp3/protocols/protocol_align_volume.py,sha256=C7FxrmwWxN_L2eX8BaP9hkvKcuKLZo1W88IswtGyh8U,20398
-xmipp3/protocols/protocol_align_volume_and_particles.py,sha256=g5dpZfq_iggeTFt2-3iGvc8zFQY_5EaiBg0gycEKPLw,10735
+xmipp3/protocols/__init__.py,sha256=eqlQGTcOi8y_bjOV_ikQ7sXNe3HmHEHT8WrlTyI5los,8348
+xmipp3/protocols/protocol_align_volume.py,sha256=09LvVV_O4ecEe2_KUNtl4se5c_kLogtdARhlvZY9ZeI,20395
+xmipp3/protocols/protocol_align_volume_and_particles.py,sha256=ZgXh8sy_oQPX84L1sPz3I9BOW6fXrP4L247mhFr31mc,11144
 xmipp3/protocols/protocol_analyze_local_ctf.py,sha256=O1_xWXuKDRGvhhd-BQ1DRMKti_KDqNN_kALzUhvN3DQ,7446
 xmipp3/protocols/protocol_angular_graph_consistency.py,sha256=aK-59_JQ849_-drD_R5NjhW9lSwy0-4WtB0Ig5UyLgQ,30300
 xmipp3/protocols/protocol_apply_alignment.py,sha256=M4bR36OxWryyhwHeQOBNrrLngw-CVnT5_4DX48bivoE,6119
@@ -66,35 +72,35 @@ xmipp3/protocols/protocol_apply_tilt_to_ctf.py,sha256=xEBtcn4SOBQIzPxBy0CMsVmiYM
 xmipp3/protocols/protocol_apply_transformation_matrix.py,sha256=TJJ7IQK_FM_-3488iBCH6JQSnBLBhPg78mYXN2E2PAk,4891
 xmipp3/protocols/protocol_apply_zernike3d.py,sha256=S1Rdw-JuE279iqfWZZqWtENc59LFCecxrkFQ9PX7iBI,10639
 xmipp3/protocols/protocol_assignment_tilt_pair.py,sha256=A1RtvoWVURIk-K8KykT0mIKNMR7UXTQKrHOkDTCbAUw,10403
-xmipp3/protocols/protocol_break_symmetry.py,sha256=OZvOOsyFMX-pdk69rYo546AxvRZtRFs0GmuT9Vkv6mc,6183
+xmipp3/protocols/protocol_break_symmetry.py,sha256=8Zs5SdOVGfnzmHRlmMuFgBfp8woCL32kx3EzdK1JtNA,6214
 xmipp3/protocols/protocol_center_particles.py,sha256=XZoeqPJXHwiahvrNBptSChyjh9i03JnWC9_Z0EIG36w,11323
 xmipp3/protocols/protocol_cl2d.py,sha256=DcZS9gvSSDrTbYOkZRT8HD4VFloEe_9TnR0AKDz4ikU,27586
 xmipp3/protocols/protocol_cl2d_align.py,sha256=vzOWv3UcMCQEYvOBNXQTDM6TNbFaGSul5IumWpo2K5M,8430
 xmipp3/protocols/protocol_cl2d_clustering.py,sha256=og3YHWD-MmZF6c0KtjTJyWkVqSPeevMptGC1uaLdVxw,13428
 xmipp3/protocols/protocol_classes_2d_mapping.py,sha256=oq6me8X4v4qFJt-GtJ4S1y64qkPCmUVWHkfMgK8XCcA,18032
-xmipp3/protocols/protocol_classify_pca.py,sha256=qZ4KRvVRlW717zN7BIwu6VIaErwbBpj4aqJ9IruzR6Y,21272
-xmipp3/protocols/protocol_classify_pca_streaming.py,sha256=MD7LmJPEoXYyRux-vBBup1rPeBnGIZIQ5N2Pe1eSGQI,23238
+xmipp3/protocols/protocol_classify_pca.py,sha256=58rnQDSYrOytyqHyD4N2r8ajGmBl4moV5ul7fsdsXxQ,21194
+xmipp3/protocols/protocol_classify_pca_streaming.py,sha256=xqG0QT2TbPjxaLTZBpMe8pX1KqwxAw0MvELEkMY6TsE,23409
 xmipp3/protocols/protocol_compare_angles.py,sha256=NIoQjym4aH3BsMJ7RaMmyswEl9gHkxMnnkQQJdAQaCw,8034
-xmipp3/protocols/protocol_compare_reprojections.py,sha256=HNoQtRT_k0MslTbGWBVQfi9M3Sz2QMZmSMinFGCI1uI,31253
-xmipp3/protocols/protocol_compute_likelihood.py,sha256=FI3t-oweSeurs-sX6KW38rq_ndNkWdp91Gaj2V5fv3M,16672
+xmipp3/protocols/protocol_compare_reprojections.py,sha256=YLSw-OsDQKfh8aEDIjCqxtJdtcFarFAzInUMw4ifwR8,31266
+xmipp3/protocols/protocol_compute_likelihood.py,sha256=0KDAVsDLSYWb1vjk7u8L0411DwbO4N4iBxqBiaPwdRg,16673
 xmipp3/protocols/protocol_consensus_classes.py,sha256=En9qEsEpkRqXE0BUOHvJI8b6VTrsZfpgd2x2GTj32eU,24604
 xmipp3/protocols/protocol_consensus_local_ctf.py,sha256=ws-CHWd1omLJB0Pkan240rOh8zW3HIzEuUAo6qKPMdI,10066
-xmipp3/protocols/protocol_convert_pdb.py,sha256=Kv3GVWP1wnPcNhh6q80eD-S82N-KhLjE-_fcHJDvbMo,16674
+xmipp3/protocols/protocol_convert_pdb.py,sha256=HEelrNfwox5CRH0QiSMF9cyuLwi4OIAs6_FaUTexM88,16671
 xmipp3/protocols/protocol_core_analysis.py,sha256=Bt2cgf4PGZB_HjmthRtdIQGT7ri-pV5vNRChm07oHB4,9919
 xmipp3/protocols/protocol_create_gallery.py,sha256=80FMOW9ayhB_bGdXn8LNO7n6JmTb1w0heLoM14AcXg4,8750
 xmipp3/protocols/protocol_ctf_consensus.py,sha256=PAMa5pIa35TDRWwaMZJHiy_GkI7fKhN_DZiDu23Lgus,39770
+xmipp3/protocols/protocol_ctf_correct_phase.py,sha256=DSX7MvGYUuxgLAj4VMlGa_bqqZ27GEZEpk1PBkz3Fiw,3780
 xmipp3/protocols/protocol_ctf_correct_wiener2d.py,sha256=VsgUUq0AgvYqfTCO9Gmh9IvsFdXzZZ2gntrnlIV1qRA,6105
 xmipp3/protocols/protocol_ctf_defocus_group.py,sha256=6x_UHiuA9WfPBhd_8rfg09Cy_j4pr6o5RCWTMMz-DPo,8333
-xmipp3/protocols/protocol_ctf_micrographs.py,sha256=VzMgMBrVzTsg_JIgAYhWR91z0KH_ABBqIrNm-UFOCSo,29288
-xmipp3/protocols/protocol_deep_center.py,sha256=JK7ojXWyGhEA6t_KmRdq3vqilkBVMWk_c7Kndj_MG_Y,6796
-xmipp3/protocols/protocol_deep_center_predict.py,sha256=F45luJp8MTGwmqenTagZJKfeatwyt-k7YnvnjmTvAFk,7183
-xmipp3/protocols/protocol_deep_hand.py,sha256=JlzndftDjPbgAYNHSVSv5ZQCOnZFCC1SxDm8kwfbn10,7778
-xmipp3/protocols/protocol_deep_micrograph_screen.py,sha256=9B9BDIgcO8escgW4H6Nnl4tqOVIQVaoxb26gBCYm6eU,22231
+xmipp3/protocols/protocol_ctf_micrographs.py,sha256=Zpfr5q-MV6veZ9VLvTuw2BpYMNfASXEa79ooKoa-RXw,29056
+xmipp3/protocols/protocol_deep_center.py,sha256=ipLYRKQtktrUYF2O08DzxfA2YAxSAzPf6pREtDSyJlg,7042
+xmipp3/protocols/protocol_deep_center_predict.py,sha256=jgtXIXuQsNpFisNjPavTp2HJ02nghrHTzXtNqhkgXdk,7405
+xmipp3/protocols/protocol_deep_hand.py,sha256=6kN0bcwy4mJSlOSScxEuh0Ij57UkjKmzxWzHBpcqgLw,7775
+xmipp3/protocols/protocol_deep_micrograph_screen.py,sha256=vrQlZzFU1fPrW4GEscLTxK3PnPdIJprGr8wrIxlokYU,22595
 xmipp3/protocols/protocol_denoise_particles.py,sha256=_FDzQ4JlNU5_RadEq0F9TfUA8H2jvDi-0pXHcTXDkOQ,7689
 xmipp3/protocols/protocol_eliminate_empty_images.py,sha256=Xil4A_zuprSZ_LjZc79CEKib2-MrUZzxyN5bDLaYaSo,22399
-xmipp3/protocols/protocol_extract_asymmetric_unit.py,sha256=y4hgaJD9guycpMDtcXru9fEfGF6o6Y29-evJHDRqHFY,8530
-xmipp3/protocols/protocol_extract_particles.py,sha256=GtQD_YWyzlybUfZUQVQeOpodY5o8Gn0UdrOG9Uet_QQ,27556
-xmipp3/protocols/protocol_extract_particles_movies.py,sha256=uq5NtTvqe-ewFjIAaD3lN2RTaaPUgPbfjAiqnpwl13s,23298
+xmipp3/protocols/protocol_extract_asymmetric_unit.py,sha256=hBD3LCfbWA-F9zDdDiXgaJLqkkKBa8hHyPnLJulRoW8,8894
+xmipp3/protocols/protocol_extract_particles.py,sha256=3ix94W4Psu66AMLG2RwHcDS9HEZR2RDKD_W3zrYH3HU,27553
 xmipp3/protocols/protocol_extract_particles_pairs.py,sha256=Z9U_xUHZOFkOdehiK7ylG48vJsfyqebDb94avTnJ4WI,29354
 xmipp3/protocols/protocol_flexalign.py,sha256=MfRQ2RiXkSo6aMvx86bW45w4xzrD6obClz49Xlo_0kE,18900
 xmipp3/protocols/protocol_generate_reprojections.py,sha256=iOTrZBWGwxLAytfY1WHDDf3UxNuOHTv_DjNja3Txoco,9788
@@ -103,17 +109,17 @@ xmipp3/protocols/protocol_kerdensom.py,sha256=dwJB8Gs1lynymNjBRVvDbGJpz9p2dRsoTg
 xmipp3/protocols/protocol_local_ctf.py,sha256=Kv9vKC6KCt_fgiF5a-4ivKeetFQGMq05jH3vHMTLLFw,8110
 xmipp3/protocols/protocol_mics_defocus_balancer.py,sha256=eYFS65J0ft_88Ggy7xCcvWmp5UJpEADKKbpfyc7lHxo,13174
 xmipp3/protocols/protocol_ml2d.py,sha256=fOkDGOADXgMxT_GeDEf2b7F8W2GdNP8ZFCTM7DEKUxk,17214
-xmipp3/protocols/protocol_movie_alignment_consensus.py,sha256=GA5cGYKD-txUUBV1FWLr8cOtW2nIAfN7GyjGsFcTKDw,29845
+xmipp3/protocols/protocol_movie_alignment_consensus.py,sha256=l_Me5ci-6u4oeLj8SLqkCTuIpePczRjE-7GBemNnlJ0,29842
 xmipp3/protocols/protocol_movie_dose_analysis.py,sha256=noyrxzJMKq6mJtANh6SJsVmAV406kCmnEv_kLOLotPY,21013
 xmipp3/protocols/protocol_movie_gain.py,sha256=JVpYI2ZiPlI5rm1dXHDcXQSavxD6rac3OYgA9Bd4BWU,24967
-xmipp3/protocols/protocol_movie_max_shift.py,sha256=DLM_IBAo74vNgCP95qV26Ftu7bjTX9mDJ8o6632mpwo,20401
-xmipp3/protocols/protocol_movie_split_frames.py,sha256=PSqV1qEgm_i5EhE1kEnnsxfwPxb6JcbtD03mxIJt_ZU,10675
+xmipp3/protocols/protocol_movie_max_shift.py,sha256=OST41FiXVKto15THefeVbpffs0vqt5YVusvPOr5CYmQ,20634
+xmipp3/protocols/protocol_movie_split_frames.py,sha256=e-UZ7xhUIXt-HJrM8pSwhS733i9r1elv8xcG_rRenX4,10672
 xmipp3/protocols/protocol_multiple_fscs.py,sha256=Q-F-gZIIk8V8jtMB1DW1R2RbDvXloS0USg6Cy1_Wf5c,6491
 xmipp3/protocols/protocol_multireference_alignability.py,sha256=ILbYwU2rHnibzf5PGSsDGI3hJsDUnn0IzC49pOoG14M,27660
 xmipp3/protocols/protocol_normalize_strain.py,sha256=FrhVITNa_9EkZ_BC53uEVjsOKWcpp0EkFlXvBZJSmgQ,3448
 xmipp3/protocols/protocol_particle_pick.py,sha256=Kk75_SEv12796oOaRL1u80hsNzV1nzFfiOcryAxaT3Y,9784
 xmipp3/protocols/protocol_particle_pick_automatic.py,sha256=m-vuteXAlvS0cFJ4jhqTzQyBfaXsfyStrdvFGcxoPOc,12083
-xmipp3/protocols/protocol_particle_pick_consensus.py,sha256=o84KzFgn4gSohLeQXHeMrwMi3sxbG3JukKxadGDi39c,16903
+xmipp3/protocols/protocol_particle_pick_consensus.py,sha256=_88fnz6GqNY9OZFA6pLkGkaEXBkVV7ig0Nxoa7cfdD0,16900
 xmipp3/protocols/protocol_particle_pick_pairs.py,sha256=1au6SwRBRSlxEydIIbYbQXCqlZoV3GvqsWuuRw_sjYY,8521
 xmipp3/protocols/protocol_particle_pick_remove_duplicates.py,sha256=v7ts6UZkLUMiYQnrhy2sBEla9wHp6sKDcKppJjyNMoE,5371
 xmipp3/protocols/protocol_phantom_create.py,sha256=4taYHFbWZz8ysAgbU59_f9nYi5rUJtOkmQ80cz5O7BI,3664
@@ -121,52 +127,52 @@ xmipp3/protocols/protocol_pick_noise.py,sha256=YtrCLU-3VWp8jn66_7ai1cCI2q83fdbUV
 xmipp3/protocols/protocol_postProcessing_deepPostProcessing.py,sha256=7v25bFDHloCqSAcpU4cSjGn71PwTYIlf_DWhWwCm0ic,15183
 xmipp3/protocols/protocol_preprocess_micrographs.py,sha256=cLLyfIs71xXNrM1j5CEssfIvJKWGQaRrjrKnYwVew58,24281
 xmipp3/protocols/protocol_random_conical_tilt.py,sha256=QFXQ80xs1ga7Bh5vYKDi91-YICUDHiDf56taARohlUc,17203
-xmipp3/protocols/protocol_ransac.py,sha256=-5380dpVAEM8kIj0Hg-H0tNed_1gwW1GMZw80GsdQ9w,29247
+xmipp3/protocols/protocol_ransac.py,sha256=LuXx_B2YV7-RNcRAUQvpB19ogqNy67tF715N_UZ68NE,29244
 xmipp3/protocols/protocol_reconstruct_fourier.py,sha256=AuRVShI3JMCw0kWkRtrSj7o9wmmaKn_pfY0SDk1KXjE,13723
-xmipp3/protocols/protocol_reconstruct_highres.py,sha256=BYfFyzCCau6og066v-530aDbQ15nKD9-y_LHQTKKMug,108551
-xmipp3/protocols/protocol_reconstruct_significant.py,sha256=F-44KGVzhWa2eRWtz5eFPeLkfWbwo4EfiUmNbdZRYn4,26124
-xmipp3/protocols/protocol_reconstruct_swarm.py,sha256=z_g7HJ6Ix_Ov3zCzLnqkJuPb3vKq82UYCpB87Cles_E,30163
-xmipp3/protocols/protocol_resolution3d.py,sha256=cJQ7gtlpPAlPsRF5xV3-MOImLBmZeg_lnS4O1aPqzio,10453
+xmipp3/protocols/protocol_reconstruct_highres.py,sha256=nlvaC702KyiYN32cCP_XJkfd2v3MtdraNOfnKNe1BVE,106664
+xmipp3/protocols/protocol_reconstruct_significant.py,sha256=EZV5_pW_FE7e3uleneoCzdLk6jTGuf06novLADoXUPI,26121
+xmipp3/protocols/protocol_reconstruct_swarm.py,sha256=aM5KAEss87VFYsNIK4E24pmBte7I0i4oGEBaBmDOFoE,30200
+xmipp3/protocols/protocol_resolution3d.py,sha256=wuax49VfqZqS8oPSqRe541WANf_69V1um4qgK4p5OGM,10388
 xmipp3/protocols/protocol_resolution_bfactor.py,sha256=IZzSZ0hJmYynghUqgReJ-h5dxOIEBkUEeBWLPlCZSx8,8006
 xmipp3/protocols/protocol_resolution_deepres.py,sha256=MsO_hLaO79p7ubtvfoG7utKJSZQZMVu5_wBTwS7JteI,17041
 xmipp3/protocols/protocol_resolution_directional.py,sha256=WXa2ATBxqDp9n8tTEyOcVZVcz6q95hlbiwhR_JwljhE,13035
-xmipp3/protocols/protocol_resolution_fso.py,sha256=qFYhERlFv9fL3XV1cqaIEFiLfhWmRb4osv5KtgdERmE,8938
-xmipp3/protocols/protocol_resolution_monogenic_signal.py,sha256=JDgww9y2FgXF7cFe_eoHlHG7lTwzUFuXeIunUMBkgHE,17785
+xmipp3/protocols/protocol_resolution_fso.py,sha256=bGMw_Y5tFSfPipvV2UfnZOXFpQrfA6qR7CljTXp1XT0,8935
+xmipp3/protocols/protocol_resolution_monogenic_signal.py,sha256=vlYrQXTs6El4vsvc867ppXDWEzwMbtqw3xk_bmG1p98,17782
 xmipp3/protocols/protocol_rotate_volume.py,sha256=qh6-5WRVm4ccL8UoLsXCKNu5q1BHqmVR2tQ6RomipcY,4477
 xmipp3/protocols/protocol_rotational_symmetry.py,sha256=hpBuxzj54aGa283Zr3J18mMGrM1cj-3Wu3ihyh1CsVU,8326
-xmipp3/protocols/protocol_screen_deepConsensus.py,sha256=iraI6DCZhwuxidzvV9R533NFJHhLtSuGp4vzy05C3OU,88733
+xmipp3/protocols/protocol_screen_deepConsensus.py,sha256=1wMtS6HoVgNYACuQJlamLCARnNBdC_vkFBiDuBcgWqA,88793
 xmipp3/protocols/protocol_screen_particles.py,sha256=bxKG3AMK77opsr1FAR2MX4qTp2h7d3sXIqT2CCfJm34,21123
-xmipp3/protocols/protocol_shift_particles.py,sha256=S4U1W6E73YaneIIibAaD_-1-2tRbDgZgDJQYdpjklyw,8893
-xmipp3/protocols/protocol_shift_volume.py,sha256=XIewovHb2edLkbpG9N5OSNLmisowfR5nOwIa9qL3Vjc,5146
-xmipp3/protocols/protocol_simulate_ctf.py,sha256=fUmCcfFWhd1wN1ciWKhZoopuic_NnJ_zCc2l0UnPTTM,8125
+xmipp3/protocols/protocol_shift_particles.py,sha256=wscdt1Z7uP_oLsLbWu791QpktbL-8SuK2aydPLaDW9c,8952
+xmipp3/protocols/protocol_shift_volume.py,sha256=0hueHd_XMzdI7fd4Oy3oAneBpLcNs-YZBfHCwx5Cdr0,6200
+xmipp3/protocols/protocol_simulate_ctf.py,sha256=h1U6TXcqvD3VQVoIDQZLI-1tOYalwnYKCuSoMezwA_w,8122
 xmipp3/protocols/protocol_structure_map.py,sha256=DVyBCQUehz45aGprt5HjEY82-AhAkrnh_DRAii-zTyc,8798
 xmipp3/protocols/protocol_structure_map_zernike3d.py,sha256=EY7rV6vSfyxYXH3ed0FTzNsYu87Ph9klYGqlwuc0eyU,22110
-xmipp3/protocols/protocol_subtract_projection.py,sha256=4Cgszp3IMKHhlr7uuDiWVDlaDbnMekJLCzrNT2leGKM,15667
+xmipp3/protocols/protocol_subtract_projection.py,sha256=pXA4FvWH1X93D7bF8OVYi-po90uJJUfs9UcK0THdAho,15664
 xmipp3/protocols/protocol_tilt_analysis.py,sha256=wcWfvQSTI2z4cyA5vyreRvhrXWFK70UByvhqFpekOkU,24168
 xmipp3/protocols/protocol_trigger_data.py,sha256=_0eTUdR3X-Wy0D9gs2HFE5YlieMhCnS3_GMLEQB-E8U,16540
-xmipp3/protocols/protocol_validate_fscq.py,sha256=YXZ2wzQcOuFmj8iPabRntmDYxIX93wdH_j_J25wdSHE,26618
+xmipp3/protocols/protocol_validate_fscq.py,sha256=_gFhxfe751QkB089df8aKxX8QRqQ4fzmzmJtjfw6ywc,26615
 xmipp3/protocols/protocol_validate_nontilt.py,sha256=gjDfF41mtL0EIJNNN0NgYgV9KSjo8hNBYnu-jb2hT9s,16443
 xmipp3/protocols/protocol_validate_overfitting.py,sha256=QYKu8Hi6QwbbEsY5V6Riu7K7PWUpj8oS__ZjobjFe80,25116
-xmipp3/protocols/protocol_volume_adjust_sub.py,sha256=ygzID66bZbm0I-N6QxTDMyiFxUfcCUFCtWcclkE5-4w,17619
+xmipp3/protocols/protocol_volume_adjust_sub.py,sha256=-u6IXnXHHwbXf-GhU6pBlI7v7pto68C9xIDciEc0X4E,17616
 xmipp3/protocols/protocol_volume_consensus.py,sha256=miaQo_ldhwAcFefBjIk32iKFpK0SBvaPaVPviD1eoL8,5626
 xmipp3/protocols/protocol_volume_deform_zernike3d.py,sha256=E-m3oelc7OVwoe-bSK7a2u-3JjtzKu5_lgM5vNkQh8o,10318
 xmipp3/protocols/protocol_volume_local_adjust.py,sha256=XupsyYS92ClxM34d1PYK8W2X9XNpAoJRREkMWth1CU4,6051
 xmipp3/protocols/protocol_volume_local_sharpening.py,sha256=ec3YLsfRm9hH8aWkFKpGtXQEzNmqVK9julvLbrM5xRk,13518
-xmipp3/protocols/protocol_volume_strain.py,sha256=d9EH5iqz7UKzjhCar8StiBjtCfwRXNuzny_LSCZdS9w,6896
+xmipp3/protocols/protocol_volume_strain.py,sha256=mWWVaDXRJ8sOXhv9ejWySoolCuL0wpiRUxtzhegPIow,6917
 xmipp3/protocols/protocol_write_testC.py,sha256=LfUhtQeT_lsZjw7yHDa0B-m33V-UmfJYMn_fFyruPnc,3288
 xmipp3/protocols/protocol_write_testP.py,sha256=2CaljDnQFTCIq7Jg6OdQjJmWHOOGpLPgdvyaN2E6cbs,4485
 xmipp3/protocols/protocol_preprocess/__init__.py,sha256=pcMVGV30RoFawgvIE1JtD90_5XWQyYCE4wkhyvgP0Ps,2424
 xmipp3/protocols/protocol_preprocess/geometrical_mask.py,sha256=8ZFzffgXlSsth83X_xOBYcFhccZgEKhVsAJhjo7AHpA,15938
 xmipp3/protocols/protocol_preprocess/protocol_add_noise.py,sha256=3gufSX9E5jsL1NgonGuVQH_DJa4-o9pynD6vbr0uuw4,12166
 xmipp3/protocols/protocol_preprocess/protocol_create_mask2d.py,sha256=EHPUzM-iDX7ETUxAE4VSrc2Rq9Isl6dgl7teZQva4CY,4237
-xmipp3/protocols/protocol_preprocess/protocol_create_mask3d.py,sha256=EkEzJJZTBwmMRa5j5jYy22gbIvOESyjGSkxPHgk7Atc,18818
-xmipp3/protocols/protocol_preprocess/protocol_crop_resize.py,sha256=43UOyMjpVmJQN24O6iPHX3-r003Jk5SxvwoxuiH1xXU,25761
+xmipp3/protocols/protocol_preprocess/protocol_create_mask3d.py,sha256=CqcmSxRQUivPPagUG4nqRZsEBAb2FU83VGMeies-Y1o,18844
+xmipp3/protocols/protocol_preprocess/protocol_crop_resize.py,sha256=FLl2HcO7kKzpPcnePCZgxJaqtws_nUPBz6Df7xAeKVA,26899
 xmipp3/protocols/protocol_preprocess/protocol_filter.py,sha256=UYZw-r5tyu0sauMo1H00leJnAAhMaMsv9nRmQ6bGimU,23565
 xmipp3/protocols/protocol_preprocess/protocol_image_operate.py,sha256=PFBdNr4udHU-PoFpa7fYNGE4G8Dl0YUB7eSKG9-ewqA,17482
 xmipp3/protocols/protocol_preprocess/protocol_mask.py,sha256=ADRalcyCjPFZsyg64RxrWZM_5pI8lJPXfTbYzzj1GhU,12060
 xmipp3/protocols/protocol_preprocess/protocol_movie_resize.py,sha256=WfaQljG1c9UZXd-gaWRdQXeZEplLYZGWxYiuGopaqto,10942
 xmipp3/protocols/protocol_preprocess/protocol_preprocess.py,sha256=M52t9Myl8_AW01kK_pPTsPHl9fpj1ubhIaNeHX7AFjU,40599
-xmipp3/protocols/protocol_preprocess/protocol_process.py,sha256=5ZHTA1K46zm9yB-v5XRhnKVBW9YMu5VOwbW1RcTELRM,8739
+xmipp3/protocols/protocol_preprocess/protocol_process.py,sha256=LRDfkN5gXCRCRWRK_qCB8XSMDPE6_j9K2MbrH7oHVDE,8803
 xmipp3/protocols/protocol_projmatch/__init__.py,sha256=fDxNicNXSbBa3WsuFouhk3INxsdQ7mlBhEYNaypFZXw,1278
 xmipp3/protocols/protocol_projmatch/projmatch_form.py,sha256=T6qmARWQoYUbKBiw-pCTOYnoHIOpuf-qyfXVHoBzx9o,36535
 xmipp3/protocols/protocol_projmatch/projmatch_initialize.py,sha256=poaVKWbyt2Bl38XHr9qOCCCRZANALnNzAhbazXgWWz4,10650
@@ -196,16 +202,16 @@ xmipp3/tests/test_protocols_deepVolPostprocessing.py,sha256=ZUSkLaR2sRlvZoaWPYwI
 xmipp3/tests/test_protocols_deepcenter_predict.py,sha256=OUtfPqeGQcgnP5Epx89t4YuzW0d3XC7iDlsBCaQy7Bk,2952
 xmipp3/tests/test_protocols_deepres.py,sha256=rXc-kAWZ8gGGS7L8e27P-ZPsFo5BPyqZKFl25V7dWII,3635
 xmipp3/tests/test_protocols_fso.py,sha256=CrVAVoBD9UbLVKT21TB0Q-tVnZ7qEsm4zcELzDnN3CU,4274
-xmipp3/tests/test_protocols_highres.py,sha256=RnJjsSdLZtdr09DyXZnpslyJdekoXiLu7TvPfYvzZSk,6505
+xmipp3/tests/test_protocols_highres.py,sha256=zvtcvL0FYfauKNKBiEbDLE-KrwdUciqx3ZgNnRjW-ZI,6511
 xmipp3/tests/test_protocols_local_defocus.py,sha256=XGXZTas0pqhHkKfZEky7a8sqLC14rB8KqoOPD27pzZE,9067
 xmipp3/tests/test_protocols_localdeblur.py,sha256=iKf-CFwts-0yePzuztB8czbQLSYvpxHv2gT89I0RHXc,7300
 xmipp3/tests/test_protocols_monores.py,sha256=FlLhcGUIGrErRh7KKCHo48dB-zrE0i9btLQxTOb-g3U,5023
 xmipp3/tests/test_protocols_realignment_classes.py,sha256=SrMOjTRr46iN69Prhpvyh9kU7VjnxhSCn3FAdBFni9U,6399
-xmipp3/tests/test_protocols_xmipp_2d.py,sha256=2LQXlP3f6cLkg3Cb4X2zzywZbrfgJg82DIp-j1tdmW0,80175
-xmipp3/tests/test_protocols_xmipp_3d.py,sha256=88LUfNyl1OxYdPF9tocn3K_vm3NQ9_9R1grbQhiSMq4,113442
+xmipp3/tests/test_protocols_xmipp_2d.py,sha256=dfvei_Dm_mUPg3o_CE0ZSLRToC-lLXMRzLEoJ3un6iw,79759
+xmipp3/tests/test_protocols_xmipp_3d.py,sha256=vWb87wX6V3KFqAQqOwxzZL7ZgAYHOgpupUDN8DqJGCc,113439
 xmipp3/tests/test_protocols_xmipp_mics.py,sha256=bFZHcPf-tzj0Fc-VWDaOhZaAZcgIr9J_gx5iasY7rJE,61412
 xmipp3/tests/test_protocols_xmipp_movie_resize.py,sha256=XR1gYYZeDhNOkDkZhimPDbqcYwss5z-zbhJ73ZM0a5g,6494
-xmipp3/tests/test_protocols_xmipp_movies.py,sha256=ZO9xuTHY6wHz2-5iRTMHgJ0xWlsvBO1tgZv_XgNIRBs,34528
+xmipp3/tests/test_protocols_xmipp_movies.py,sha256=ILm8SxMt8zcNWHJh_2RsqRIgiyb2DqfcD0ZABhFIZxM,28098
 xmipp3/tests/test_protocols_zernike3d.py,sha256=bTXCK4wBKSJZK1KCZXec3j8y1mVLoBxE5bF3AGbOsNs,18132
 xmipp3/viewers/__init__.py,sha256=NyHVGW8GTDZ2o1rXW41bqj4XNEo6KcBRoMNktHFAHec,3647
 xmipp3/viewers/plotter.py,sha256=YHDqAs7_rbv8cXMmwmg42YeeBnesdX44awrppX3VJw0,3875
@@ -215,7 +221,7 @@ xmipp3/viewers/viewer_analyze_local_ctf.py,sha256=-Oa7flu05KxP8M6AlZRaWKCRqZljRz
 xmipp3/viewers/viewer_apply_tilt_to_ctf.py,sha256=GdKDSI1FjcgvKxOrO6BOWPaLrYpMYh2AtXxB3BEK7So,3263
 xmipp3/viewers/viewer_cl2d.py,sha256=7uBU6zYOkhYqjMNWFUPFbMOPsqWja9DaTssp_ju6AXw,8764
 xmipp3/viewers/viewer_cl2d_clustering.py,sha256=PKJbAyi_meEPgSEtOFE9vYusz0WLGaphDGeqee9BbpE,5768
-xmipp3/viewers/viewer_consensus_classes.py,sha256=En4EW8tYDS0NLmGoM9IBz_KM9PoBtDo-AqfVxmUDFeE,5434
+xmipp3/viewers/viewer_consensus_classes.py,sha256=Q9jt1bAb3ijiDuWLzlCsP2dKGfsXRuSGHQvI2kYHqlU,6286
 xmipp3/viewers/viewer_ctf_consensus.py,sha256=gosd9D2iuTUHgdlQlHIGS_HBybThR1S8SBfgM096e_8,7669
 xmipp3/viewers/viewer_deepEMHancer.py,sha256=ok5e2NfPeK8Joa0Y7Wp0GQG00Pk7AAG19xOE42A1l6c,5741
 xmipp3/viewers/viewer_deep_consensus.py,sha256=8ebETC_KyoFHFC2s_WRip1h6DxopxCKYuGndYFJaFS4,5232
@@ -237,7 +243,7 @@ xmipp3/viewers/viewer_resolution_deepres.py,sha256=M1X9wW7V4yU0BaMxezFNSHhfd4Rpj
 xmipp3/viewers/viewer_resolution_directional.py,sha256=SOnybW40HuMglekNnD-YGF2ZPMXLZuGf-AwmvRUNg98,20322
 xmipp3/viewers/viewer_resolution_fso.py,sha256=CwLUN_w0jeKbn9CBFl_XJn0MTMtfatl6Hz6IlxqbGg4,16206
 xmipp3/viewers/viewer_resolution_monogenic_signal.py,sha256=GCrWKLb9IFVcGY8zKzCNnXWy15T_jPPhM2uZjJ0un8c,11088
-xmipp3/viewers/viewer_structure_map.py,sha256=aBPfzuDAFix7NzucQrT_FLqYxBJVfq6kMnwW3DXjpuY,15910
+xmipp3/viewers/viewer_structure_map.py,sha256=bMnUfph3Nvoi_uiBNLtu4ztC-z3gw0dwey2J_xwR2zQ,23119
 xmipp3/viewers/viewer_subtract_projection.py,sha256=UPm_G_CwTUgtgzVMtNCF3NFgnfwxJSy3HmaKYW2WECE,2860
 xmipp3/viewers/viewer_swarm.py,sha256=liXSpVMNqO0YzcexF6hyl8n8V6j2t7yB8D42dHWIazk,2590
 xmipp3/viewers/viewer_validate_fscq.py,sha256=bqb_va-BjTn1LpuyOroCPX3QeL104Kh2TX9faOBTH-E,18209
@@ -247,9 +253,8 @@ xmipp3/viewers/viewer_volume_consensus.py,sha256=S7YViiZ9w5xAGhfyj1RnDypVWsQ7PKh
 xmipp3/viewers/viewer_volume_deform_zernike3d.py,sha256=BOeI7go5w2RRwGjV9kPm2U76tVJRaHww1Pl0zUCXQRw,8903
 xmipp3/viewers/viewer_volume_strain.py,sha256=4LQUrceVMB6OaAfTpFXdn3vGv-sXQzUIPDEPELYfasY,2378
 xmipp3/viewers/viewer_volume_subtraction.py,sha256=3RbwJQIaCcdzldrFODLgWlFbCips1450RDVzngLRRoU,5121
-scipion_em_xmipp-25.6.1.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-scipion_em_xmipp-25.6.1.dist-info/METADATA,sha256=mDLbPk7votlQ9eRPh8o9nOuo1vuPa9s1mTy5Ea4OtdI,1941
-scipion_em_xmipp-25.6.1.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-scipion_em_xmipp-25.6.1.dist-info/entry_points.txt,sha256=9e0I0urUxrUF7LZfZbhoATUnLuGxyJTjj81mP7FhKm8,36
-scipion_em_xmipp-25.6.1.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
-scipion_em_xmipp-25.6.1.dist-info/RECORD,,
+scipion_em_xmipp-26.0.0.dist-info/METADATA,sha256=TapL-Yr1UasE-o3eUbVXQL8kBDBpWbnVJAm2pKbRR8U,2026
+scipion_em_xmipp-26.0.0.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
+scipion_em_xmipp-26.0.0.dist-info/entry_points.txt,sha256=9e0I0urUxrUF7LZfZbhoATUnLuGxyJTjj81mP7FhKm8,36
+scipion_em_xmipp-26.0.0.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
+scipion_em_xmipp-26.0.0.dist-info/RECORD,,

{scipion_em_xmipp-25.6.1.dist-info → scipion_em_xmipp-26.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.2)
+Generator: setuptools (79.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

xmipp3/__init__.py

@@ -45,8 +45,6 @@ NVIDIA_DRIVERS_MINIMUM_VERSION = 450
 
 type_of_version = version.type_of_version
 _logo = version._logo
-_binTagVersion = version._binTagVersion
-_pluginTagVersion= version._pluginTagVersion
 _currentDepVersion = version._currentDepVersion
 __version__ = version.__version__
 
@@ -151,30 +149,33 @@ class Plugin(pwem.Plugin):
         
         # When changing dependencies, increment _currentDepVersion
         CONDA_DEPENDENCIES = [
-	        "'cmake>=3.18,<4'", #cmake-4 is not compatible with Relion compilation
+	    "'cmake>=3.18,<4'", #cmake-4 is not compatible with Relion compilation
             "hdf5>=1.18",
             "sqlite>=3",
             "fftw>=3",
             "make",
             "zlib",
             "openjdk",
-            "libtiff",
-	    "libstdcxx-ng",
+            "'libtiff<=4.5.1'",
             "libjpeg-turbo",
         ]
+
+        CONDA_LIBSTDCXX_PACKAGE = "libstdcxx-ng"
+
         if Config.isCondaInstallation():
             condaEnvPath = os.environ['CONDA_PREFIX']
             scipionEnv=os.path.basename(condaEnvPath)  # TODO: use pyworkflow method when released: Config.getEnvName()
 
             commands = CondaCommandDef(scipionEnv, cls.getCondaActivationCmd())
-            commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
+            #commands.condaInstall('-c conda-forge --yes '  + ' '.join(CONDA_DEPENDENCIES))
+            commands.condaInstall('-c conda-forge --yes '  + CONDA_LIBSTDCXX_PACKAGE)
             commands.touch("deps_installed.txt")
             env.addPackage(
                 'xmippDep', version=_currentDepVersion,
                 tar='void.tgz',
                 commands=commands.getCommands(),
                 neededProgs=['conda'],
-                default=False
+                default=True
             )
         
         if develMode:
@@ -196,16 +197,15 @@ class Plugin(pwem.Plugin):
 	            default=False
 	        )
         else:
-            xmippSrc = f'xmippSrc-{version._binTagVersion}'
+            xmippSrc = f'xmipp3-{version._binVersion}'
             installCommands = [
                 (f'cd .. && rm -rf {xmippSrc} && '
-                f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
+                f'git clone {XMIPP_GIT_URL} -b {version._binVersion} {xmippSrc} && '
                 f'cd {xmippSrc} && '
-                f'git checkout {version._binTagVersion} && '
                 f'./xmipp --production True ', COMPILE_TARGETS)
             ]
             env.addPackage(
-	                'xmippSrc', version=version._binTagVersion,
+	                'xmipp3', version=version._binVersion,
 	                tar='void.tgz',
 	                commands=installCommands,
 	                neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
@@ -225,7 +225,7 @@ class Plugin(pwem.Plugin):
 
         isBundle = (os.path.isdir(os.path.join(bundleDir, 'src')) and
                     os.path.isfile(os.path.join(bundleDir, 'xmipp')))
-        
+        print(f'pluginDir: {pluginDir}\n, bundleDir: {bundleDir}\n, isBundle: {isBundle}')
         return bundleDir if isBundle else None
 
 def getNvidiaDriverVersion(plugin):

xmipp3/constants.py

@@ -28,7 +28,7 @@ This modules contains constants related to Xmipp3 protocols
 """
 
 # ------------------ Constants values --------------------------------------
-XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp.git'
+XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp3.git'
 XMIPP_URL = 'https://github.com/i2pc/scipion-em-xmipp'
 XMIPP_HOME = 'XMIPP_HOME'
 NMA_HOME = 'NMA_HOME'

xmipp3/legacy/tests/test_protocols_xmipp_movies.py

@@ -227,3 +227,137 @@ class TestOFAlignment2(TestXmippBase):
                              "been created.")
 
 
+class TestExtractMovieParticles(BaseTest):
+	@classmethod
+	def setData(cls):
+		cls.ds = DataSet.getDataSet('movies')
+
+	@classmethod
+	def runImportMovies(cls, pattern, **kwargs):
+		""" Run an Import micrograph protocol. """
+		# We have two options: passe the SamplingRate or
+		# the ScannedPixelSize + microscope magnification
+		params = {'samplingRate': 1.14,
+		          'voltage': 300,
+		          'sphericalAberration': 2.7,
+		          'magnification': 50000,
+		          'scannedPixelSize': None,
+		          'filesPattern': pattern
+		          }
+		if 'samplingRate' not in kwargs:
+			del params['samplingRate']
+			params['samplingRateMode'] = 0
+		else:
+			params['samplingRateMode'] = 1
+
+		params.update(kwargs)
+
+		protImport = cls.newProtocol(ProtImportMovies, **params)
+		cls.launchProtocol(protImport)
+		return protImport
+
+	@classmethod
+	def setUpClass(cls):
+		setupTestProject(cls)
+		cls.setData()
+		cls.protImport1 = cls.runImportMovies(
+			cls.ds.getFile('qbeta/qbeta.mrc'),
+			magnification=50000)
+		cls.protImport2 = cls.runImportMovies(cls.ds.getFile('cct/cct_1.em'),
+		                                      magnification=61000)
+
+	# def _checkMicrographs(self, protocol, goldDimensions):
+	#     self.assertIsNotNone(getattr(protocol, 'outputMicrographs', None),
+	#                          "Output SetOfMicrographs were not created.")
+	#     mic = protocol.outputMicrographs[1]
+	#     x, y, _ = mic.getDim()
+	#     dims = (x, y)
+	#     msgError = "The dimensions must be %s and it is %s"
+	#     self.assertEqual(goldDimensions, dims,
+	#                      msgError % (goldDimensions, dims))
+	#
+	def _checkAlignment(self, movie, goldRange, goldRoi):
+		alignment = movie.getAlignment()
+		range = alignment.getRange()
+		msgRange = "Alignment range must be %s %s and it is %s (%s)"
+		self.assertEqual(goldRange, range,
+		                 msgRange % (
+			                 goldRange, range, type(goldRange), type(range)))
+		roi = alignment.getRoi()
+		msgRoi = "Alignment ROI must be %s (%s) and it is %s (%s)"
+		self.assertEqual(goldRoi, roi,
+		                 msgRoi % (goldRoi, roi, type(goldRoi), type(roi)))
+
+	def test_qbeta(self):
+		movAliProt = self.newProtocol(XmippProtFlexAlign,
+		                              alignFrame0=2, alignFrameN=6,
+		                              doSaveAveMic=True)
+		movAliProt.inputMovies.set(self.protImport1.outputMovies)
+		self.launchProtocol(movAliProt)
+
+		self._checkAlignment(movAliProt.outputMovies[1],
+		                     (2, 6), [0, 0, 0, 0])
+
+		importPick = self.newProtocol(ProtImportCoordinates,
+		                              importFrom=ProtImportCoordinates.IMPORT_FROM_XMIPP,
+		                              filesPath=self.ds.getFile('qbeta/'),
+		                              filesPattern='*.pos', boxSize=320,
+		                              invertX=False,
+		                              invertY=False
+		                              )
+		importPick.inputMicrographs.set(movAliProt.outputMicrographs)
+		importPick.setObjLabel('import coords from xmipp ')
+		self.launchProtocol(importPick)
+
+		protExtract = self.newProtocol(XmippProtExtractMovieParticles,
+		                               boxSize=320, frame0=2, frameN=6,
+		                               applyAlignment=True, doInvert=True)
+		protExtract.inputMovies.set(movAliProt.outputMovies)
+		protExtract.inputCoordinates.set(importPick.outputCoordinates)
+		protExtract.setObjLabel('extract with alignment')
+		self.launchProtocol(protExtract)
+
+		self.assertIsNotNone(getattr(protExtract, 'outputParticles', None),
+		                     "Output SetOfMovieParticles were not created.")
+
+		size = protExtract.outputParticles.getSize()
+		self.assertEqual(size, 135, 'Number of particles must be 135 and its '
+		                            '%d' % size)
+
+	def test_cct(self):
+		movAliProt = self.newProtocol(XmippProtFlexAlign,
+		                              alignFrame0=2, alignFrameN=6,
+		                              doSaveAveMic=True)
+		movAliProt.inputMovies.set(self.protImport2.outputMovies)
+		self.launchProtocol(movAliProt)
+
+		self._checkAlignment(movAliProt.outputMovies[1],
+		                     (2, 6), [0, 0, 0, 0])
+
+		importPick = self.newProtocol(ProtImportCoordinates,
+		                              importFrom=ProtImportCoordinates.IMPORT_FROM_XMIPP,
+		                              filesPath=self.ds.getFile('cct/'),
+		                              filesPattern='*.pos', boxSize=320,
+		                              invertX=False,
+		                              invertY=False
+		                              )
+		importPick.inputMicrographs.set(movAliProt.outputMicrographs)
+		importPick.setObjLabel('import coords from xmipp ')
+		self.launchProtocol(importPick)
+
+		protExtract = self.newProtocol(XmippProtExtractMovieParticles,
+		                               boxSize=320, frame0=3, frameN=6,
+		                               applyAlignment=False, doInvert=True)
+		protExtract.inputMovies.set(movAliProt.outputMovies)
+		protExtract.inputCoordinates.set(importPick.outputCoordinates)
+		protExtract.setObjLabel('extract without alignment')
+		self.launchProtocol(protExtract)
+
+		self.assertIsNotNone(getattr(protExtract, 'outputParticles', None),
+		                     "Output SetOfMovieParticles were not created.")
+
+		size = protExtract.outputParticles.getSize()
+		self.assertEqual(size, 88, 'Number of particles must be 135 and its '
+		                           '%d' % size)
+
+

xmipp3/logParser.py

@@ -0,0 +1,53 @@
+# **************************************************************************
+# *
+# * Authors:     Alberto Garcia Mena (alberto.garcia@cnb.csic.es)
+# *
+# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address 'scipion@cnb.csic.es'
+# *
+# **************************************************************************
+
+'''
+Script to collect all failled attempts from aspecific release of Xmipp and return a json with just the logs reported
+Requires a json generated on https://xmipp.i2pc.es/api/attempts/filters/?user__userId=&xmipp__branch=v3.25.06.0-Rhea&returnCode=&returnCode_not=0 (get-> json save)
+After this scxript, ask any IA:
+ChatGPT Question: This is a JSON file with the logs of the installation failures of Xmipp. Can you make a summary of the most common errors?
+Ommit the Matlab errors and warnings, report the percent of each kind of error
+'''
+
+import json
+import random
+
+jsonpath = '/home/agarcia/Downloads/Rhea.json'
+jsonGenerated = '/home/agarcia/Downloads/RheaJustLogs.json'
+with open(jsonpath, "r") as f:
+    data = json.load(f)
+
+# data is now a list of dicts
+print(f"Number of entries: {len(data)}")
+
+logs = [entry["logTail"] for entry in data if "logTail" in entry]
+
+# pick a random subset of 100 entries
+subset = random.sample(logs, min(400, len(logs)))
+
+# write to new JSON file
+with open(jsonGenerated, "w") as f:
+    json.dump(subset, f, indent=4, ensure_ascii=False)

xmipp3/protocols/__init__.py

@@ -52,13 +52,13 @@ from .protocol_create_gallery import XmippProtCreateGallery
 from .protocol_ctf_consensus import XmippProtCTFConsensus
 from .protocol_ctf_micrographs import XmippProtCTFMicrographs
 from .protocol_ctf_correct_wiener2d import XmippProtCTFCorrectWiener2D
+from .protocol_ctf_correct_phase import XmippProtCTFCorrectPhase2D
 from .protocol_consensus_classes import XmippProtConsensusClasses
 from .protocol_denoise_particles import XmippProtDenoiseParticles
 from .protocol_deep_micrograph_screen import XmippProtDeepMicrographScreen
 from .protocol_eliminate_empty_images import (XmippProtEliminateEmptyParticles,
                                               XmippProtEliminateEmptyClasses)
 from .protocol_extract_particles import XmippProtExtractParticles
-from .protocol_extract_particles_movies import XmippProtExtractMovieParticles
 from .protocol_extract_particles_pairs import XmippProtExtractParticlesPairs
 from .protocol_extract_asymmetric_unit import XmippProtExtractUnit
 from .protocol_helical_parameters import XmippProtHelicalParameters

xmipp3/protocols/protocol_align_volume.py

@@ -51,7 +51,7 @@ class XmippProtAlignVolume(ProtAlignVolume):
      """
     _label = 'align volume'
     nVols = 0
-    _devStatus = UPDATED
+    _devStatus = PROD
     OUTPUT_NAME1 = "outputVolume"
     OUTPUT_NAME2 = "outputVolumes"
     _possibleOutputs = {OUTPUT_NAME1: Volume,