scipion-em-xmipp 24.6.0.0__py3-none-any.whl → 24.12.2__py3-none-any.whl

{scipion_em_xmipp-24.6.0.0.dist-info → scipion_em_xmipp-24.12.2.dist-info}/METADATA

@@ -1,21 +1,22 @@
 Metadata-Version: 2.1
 Name: scipion-em-xmipp
-Version: 24.6.0.0
-Summary: Plugin to use Xmipp programs within the Scipion framework (see https://scipion-em.github.io/docs/).
+Version: 24.12.2
+Summary: Plugin to use Xmipp programs within the Scipion framework (see https://xmipp.i2pc.es/).
 Home-page: https://github.com/i2pc/scipion-em-xmipp
 Author: I2PC
-Author-email: scipion@cnb.csic.es
+Author-email: xmipp@cnb.csic.es
 License: UNKNOWN
 Keywords: scipion cryoem imageprocessing scipion-3.0
 Platform: UNKNOWN
-Requires-Dist: scipion-pyworkflow >=3.0.31
-Requires-Dist: scikit-learn ==0.22
+Requires-Dist: scipion-pyworkflow>=3.0.31
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: scikit-image
 Requires-Dist: scipion-em
-Requires-Dist: scipy <=1.10.0
+Requires-Dist: scipion-app
+Requires-Dist: scipy<=1.10.0
 Requires-Dist: joblib
 Requires-Dist: peppercorn
 Requires-Dist: plotter
-Requires-Dist: scons
 Requires-Dist: PyWavelets
 
 [![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-24.6.0.0.dist-info → scipion_em_xmipp-24.12.2.dist-info}/RECORD

@@ -1,65 +1,69 @@
-xmipp3/__init__.py,sha256=Bc3CesJmNp5xxqL5CBfhPOWrkf14NyW7W0rm4htDsrQ,13303
+xmipp3/__init__.py,sha256=3845iUcBXhJdilaAZh_oB76sDuzfmVms4TiFzVWDpV4,12226
 xmipp3/base.py,sha256=pFu7FZjm4WeqWbLZJwbmGH3-2YixAIpKyWMFvVrsBYc,21220
 xmipp3/bibtex.py,sha256=YZjuuB_9RC4QOOy5r86cRX3ze2EWz43iGzIDQvtu5HQ,28310
-xmipp3/constants.py,sha256=ND8PUJyUIP3IS3kbq0tZqk77Yq0c4WotRUj_r2gEDxo,3833
+xmipp3/checkProtocolsConf.py,sha256=eJhADp1lv3Mdwe5yYdsVJcVzjelUCqoLHs43XSGzrDo,4428
+xmipp3/constants.py,sha256=SjO3ViST8YrLIn49QqymQNrNwzM1wzG9VOupvnyM-_U,3953
 xmipp3/programs.py,sha256=yrMD0EHEq5j_ODCeINbaCp4CEqSgkmioan1O1mAgPY0,11968
-xmipp3/protocols.conf,sha256=Dwg5S_PBQV9wy5n5CmEppB75P4Nmur2l1FsKLrMCde8,12631
+xmipp3/protocols.conf,sha256=6zuA9QdZ_HVaPc0mxqn3oGWJVQtdCVZIJeceMYw4J6I,15148
 xmipp3/utils.py,sha256=JKuEdR40rn6pdm0puwsgzItbNnrFL4sa7pBymVtRzLM,9125
+xmipp3/version.py,sha256=ZhxJ-ScXQm8YwCeHUy6dEH_NToDwkMQr5jx6moVa13s,1807
 xmipp3/wizards.py,sha256=kS2ctLuy46m-8XPWrd2705V9Gxbhf4UBa4vKJ8eqius,20343
 xmipp3/xmipp_logo.png,sha256=ggrFNUy5UEBjvKfNvu0T14Kzolnhc-ij9AQ734R27MY,84496
 xmipp3/convert/__init__.py,sha256=y231wRpfDySMgyjLi6xYuO3hTG1NZBNnMRT7dNnYqu8,1211
-xmipp3/convert/convert.py,sha256=ikxH7kMUvUUbmikalhPJ5tG8rWTCEGPhx73PoAFQXB0,62304
+xmipp3/convert/convert.py,sha256=_8wbBzv714l2rfQyj1pvjXP9VPLs7gvk_fiFJYzmctU,63217
 xmipp3/convert/dataimport.py,sha256=ssmMLKU1qXDuqjStNJv-zfYNJAJ-0k7EzNyF4jf91IU,13292
 xmipp3/convert/io_coordinates.py,sha256=ZUKEbL7DjJ0jDVJzs2Nnc-sX7QYuAyGSponhP6WYMDI,1963
-xmipp3/protocols/__init__.py,sha256=cE4L0pNHeQdeZsEbs9dHNa-6gPdM1V5G23-OMuWlCUE,8301
+xmipp3/protocols/__init__.py,sha256=V34OLNcejL0Hywls2IoFAcD9GmgaSckUOK-ZNwsMGS8,8406
 xmipp3/protocols/protocol_align_volume.py,sha256=uxFtsb9cB0tz9QkyXvR3pK5457x9sq9F-qyeuOeA2go,19070
 xmipp3/protocols/protocol_align_volume_and_particles.py,sha256=g5dpZfq_iggeTFt2-3iGvc8zFQY_5EaiBg0gycEKPLw,10735
 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_angular_resolution_alignment.py,sha256=EsKm1PfGkkpnzoKuhZqM-e1_99_XVtIBOIGhlgg45qM,8521
 xmipp3/protocols/protocol_apply_alignment.py,sha256=TL89xGiYtPN5mlEhU4R-6yLEzjxIyx2TStiTyXdkvKw,5958
+xmipp3/protocols/protocol_apply_tilt_to_ctf.py,sha256=WiWBip-lU4ApdDbilQbckSf_ueXmNhcfSKAUxhH1EeY,5287
 xmipp3/protocols/protocol_apply_transformation_matrix.py,sha256=TJJ7IQK_FM_-3488iBCH6JQSnBLBhPg78mYXN2E2PAk,4891
 xmipp3/protocols/protocol_apply_zernike3d.py,sha256=aHb-6oFCLIZV49OXlft_VQgmcO9vd65-g-KFPK-Arbw,10506
 xmipp3/protocols/protocol_assignment_tilt_pair.py,sha256=4bjhPZbffm2jIZV4LLbrw-_fhNbzZVPf1UmzbqhpK_o,10332
 xmipp3/protocols/protocol_break_symmetry.py,sha256=OZvOOsyFMX-pdk69rYo546AxvRZtRFs0GmuT9Vkv6mc,6183
 xmipp3/protocols/protocol_center_particles.py,sha256=2ug42YlvD7PidOLC1EL6U4b-WFm9i6UF8ggn_ksC14E,11159
-xmipp3/protocols/protocol_cl2d.py,sha256=ovh25H8QbcdsmqV1J0M-1d3vzbQYnTT6WH2O2hkohEg,27500
+xmipp3/protocols/protocol_cl2d.py,sha256=yxILvNNWL_1Mazgo9_r4bQopGSMsF0c4bZ0H7l1awMQ,27497
 xmipp3/protocols/protocol_cl2d_align.py,sha256=RF_WVqNMnLGXALW5LyIQ43JmoysSyYcrV5vOsnef0oY,8279
+xmipp3/protocols/protocol_cl2d_clustering.py,sha256=MjYS5w_lU9Jd9SPRE_8ttWYeeDkwnK3mb_o9YUku8s0,13334
 xmipp3/protocols/protocol_classes_2d_mapping.py,sha256=oq6me8X4v4qFJt-GtJ4S1y64qkPCmUVWHkfMgK8XCcA,18032
-xmipp3/protocols/protocol_classify_pca.py,sha256=PepVs7BOgJ-0mbZLjr-gJN58X3n51e3ujbN5AkxUPvU,20288
-xmipp3/protocols/protocol_classify_pca_streaming.py,sha256=Lpm33qPG4gR9xW9MYqdsHiFOV_jzEsqyw6vRx2sZRTw,22015
+xmipp3/protocols/protocol_classify_pca.py,sha256=M-dHSHT-qrPzBbW84Olm91ZxTI2Lvl4LexIBNWYh7zI,20340
+xmipp3/protocols/protocol_classify_pca_streaming.py,sha256=aMu5j_QC_NKsKHwthJEtoEYL4a4bNfILgmhZaf2RS0g,22083
 xmipp3/protocols/protocol_compare_angles.py,sha256=NIoQjym4aH3BsMJ7RaMmyswEl9gHkxMnnkQQJdAQaCw,8034
-xmipp3/protocols/protocol_compare_reprojections.py,sha256=H4QN60KdXlspxv_SR4JF3YVT01tovgGv6dfDTf0OENc,31250
+xmipp3/protocols/protocol_compare_reprojections.py,sha256=HNoQtRT_k0MslTbGWBVQfi9M3Sz2QMZmSMinFGCI1uI,31253
 xmipp3/protocols/protocol_consensus_classes.py,sha256=En9qEsEpkRqXE0BUOHvJI8b6VTrsZfpgd2x2GTj32eU,24604
 xmipp3/protocols/protocol_consensus_local_ctf.py,sha256=qJrZ1GVJgaNmX60_GvbUDg-qg3FqXnfoLXWhfoXiJss,9953
-xmipp3/protocols/protocol_convert_pdb.py,sha256=tSDLzyL7xidVToD3bw-9yi80U9BCLOR6RWxr0bWaRj8,15488
+xmipp3/protocols/protocol_convert_pdb.py,sha256=KfilRGZ5GQKrYOCw9N8FCMzAhTe6FR9DWyOBnk-gUgc,15782
 xmipp3/protocols/protocol_core_analysis.py,sha256=Bt2cgf4PGZB_HjmthRtdIQGT7ri-pV5vNRChm07oHB4,9919
-xmipp3/protocols/protocol_create_gallery.py,sha256=GwuJxJLkPlxZxUSt-J8oDgPN7wWmFBd4iPENcve_JIY,5970
-xmipp3/protocols/protocol_ctf_consensus.py,sha256=_ug1EQG9COSWK-VHIsMXXDthK4tbRPgt7QUqJyyYrFQ,42582
+xmipp3/protocols/protocol_create_gallery.py,sha256=ldOimkkf1D9cLNuexvFTxkcVJQr1YRETidTbXmp-lF8,8753
+xmipp3/protocols/protocol_ctf_consensus.py,sha256=WRSYKdD_nOoqIYpEJJOhCygi2PDcoUmSzSsK4dyajwM,39582
 xmipp3/protocols/protocol_ctf_correct_wiener2d.py,sha256=thDaon-jYBeXbGM_UiEwfLCeURPwD_7ycgzUzNc3T5g,5819
-xmipp3/protocols/protocol_ctf_defocus_group.py,sha256=c_it4w5tJAxC9HpMzcYp58cZLRXSNS4hjgeJ_L6iKkI,8304
-xmipp3/protocols/protocol_ctf_micrographs.py,sha256=R0ocHeLuAAiwkvhfoZF8votSXKfv1f2Vjny7mmdpf2g,28384
-xmipp3/protocols/protocol_deep_center.py,sha256=GGivftHKyg1wlLnfS0im9IS1NIKxXr8Fky3Yt2-3ieQ,6742
+xmipp3/protocols/protocol_ctf_defocus_group.py,sha256=6x_UHiuA9WfPBhd_8rfg09Cy_j4pr6o5RCWTMMz-DPo,8333
+xmipp3/protocols/protocol_ctf_micrographs.py,sha256=5bOIKOm3bdx6Qmko4Qa7o6FduZxFHvdJ7pmzwcoZCCw,28979
+xmipp3/protocols/protocol_deep_center.py,sha256=JK7ojXWyGhEA6t_KmRdq3vqilkBVMWk_c7Kndj_MG_Y,6796
+xmipp3/protocols/protocol_deep_center_predict.py,sha256=qxC0aDL-oz7-9LwaIcLtb1vhY9J9t254wta_bV-mpBU,6788
 xmipp3/protocols/protocol_deep_hand.py,sha256=KeKV6DHqpua1GoL3dWojYhwAHEiUxXy5Mdkr0at77ag,7185
 xmipp3/protocols/protocol_deep_micrograph_screen.py,sha256=AL9c6dqsdSOA1MCEOzYcWd5mtoCfyJyioIXALmJ4Scw,22068
 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_enrich.py,sha256=pymPJpNAHUNtECe89-pdzcVmkdNbVN7kp1PGz9NgwYg,25080
 xmipp3/protocols/protocol_extract_asymmetric_unit.py,sha256=1XOA2waEA0EY8z7iB-2ivJXbiNDegzIyYmkOxTpXseM,8356
-xmipp3/protocols/protocol_extract_particles.py,sha256=Mt9gOGR2c6wQ0JC0seFNRFKv1teXyASpJxw9FpbYABg,26486
+xmipp3/protocols/protocol_extract_particles.py,sha256=iQ6xlMtYpWflOGcDgYZJ4XxUi-aZCassmFnPMAe69qI,26483
 xmipp3/protocols/protocol_extract_particles_movies.py,sha256=DYHNx0RRvcvnEXD6rnEYnp7gbv-hNjtjhKvK47MwpHw,23165
 xmipp3/protocols/protocol_extract_particles_pairs.py,sha256=Cg0I_hptAErRXSrtDZnSrUDMx_P2NFgrFV34pUcQFoM,29349
-xmipp3/protocols/protocol_flexalign.py,sha256=FCGlCLc0Rk1HomaFYj9l_DiYPrx1K-7f5DmlzSBhjzI,18498
+xmipp3/protocols/protocol_flexalign.py,sha256=9Gw-TCiOLUM2uG_j0NlU9CYonSTBNyimPUhlur5ClrY,18815
 xmipp3/protocols/protocol_generate_reprojections.py,sha256=iOTrZBWGwxLAytfY1WHDDf3UxNuOHTv_DjNja3Txoco,9788
 xmipp3/protocols/protocol_helical_parameters.py,sha256=aExrXYis9jmRx4GOagy1TRdTaUeK1nkX3akHSS41aoQ,9841
 xmipp3/protocols/protocol_kerdensom.py,sha256=dwJB8Gs1lynymNjBRVvDbGJpz9p2dRsoTgkT-1B08Fs,12393
 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=BcRB_LfPvJNkDK8BR4ejtwuRKEkqD5V5yTqUPyiihPA,25019
-xmipp3/protocols/protocol_movie_dose_analysis.py,sha256=EEhCwurO4EoNiAyV53ykneYVSPhAh4sls-0Ka4A7g_4,17040
-xmipp3/protocols/protocol_movie_gain.py,sha256=tc1GU3-VbV1fkxXzPY0nCGMMKO0lEdtt6HCWKR_azKs,24802
-xmipp3/protocols/protocol_movie_max_shift.py,sha256=zrzZAh-mBWNfVJ-2w12EmbaJ7IYBuQOsdqxRzJkebqE,17726
-xmipp3/protocols/protocol_movie_opticalflow.py,sha256=js8Tk6MR47T7wlCkQn2dUb9iQu79UWOnWfEwqNNsZrw,18059
+xmipp3/protocols/protocol_movie_alignment_consensus.py,sha256=UJD_baOMbc-Nls2Oy8YO26pNtKNDoT4jS0pKh4DH90E,25020
+xmipp3/protocols/protocol_movie_dose_analysis.py,sha256=71E8h0h4HkpZT9j_X3ZLH5S68VHgydIa82Al_ade8n0,20516
+xmipp3/protocols/protocol_movie_gain.py,sha256=JVpYI2ZiPlI5rm1dXHDcXQSavxD6rac3OYgA9Bd4BWU,24967
+xmipp3/protocols/protocol_movie_max_shift.py,sha256=9ORlwtpGycMVhqByje1yeqbd6LmYt41sxTMQv9dHZKI,20188
 xmipp3/protocols/protocol_movie_split_frames.py,sha256=yx4DryyQDyyqLwp0ckyHjy-_aDBMjdvIIBCZ80Xe4OI,7175
 xmipp3/protocols/protocol_multiple_fscs.py,sha256=Q-F-gZIIk8V8jtMB1DW1R2RbDvXloS0USg6Cy1_Wf5c,6491
 xmipp3/protocols/protocol_multireference_alignability.py,sha256=ILbYwU2rHnibzf5PGSsDGI3hJsDUnn0IzC49pOoG14M,27660
@@ -75,8 +79,8 @@ xmipp3/protocols/protocol_postProcessing_deepPostProcessing.py,sha256=RqcwXuj22B
 xmipp3/protocols/protocol_preprocess_micrographs.py,sha256=eKu-Hdtd8lsxuT1J7JW_N3AJSESkZxL2-HF-iU5E3SM,23961
 xmipp3/protocols/protocol_random_conical_tilt.py,sha256=R5PrC9JGPWylpBrZ70_VPpN5zySPXI6YM6Mdlbpib3Y,17030
 xmipp3/protocols/protocol_ransac.py,sha256=-Ih7qjWcjzKgyUEphVk7bpd9S1fMFaO2AfYalzd2fGk,28957
-xmipp3/protocols/protocol_reconstruct_fourier.py,sha256=mZ-kCM2V1hhEaXVuCq-_LbyhlUudZ3t1VeB0-fpT2Mc,12271
-xmipp3/protocols/protocol_reconstruct_highres.py,sha256=WGCuJvEhFEFtLg_jD8wDdpjz1KS4ckHYX7tNpfhhw8A,107816
+xmipp3/protocols/protocol_reconstruct_fourier.py,sha256=3cY-qb8n5Cjs9DyLfUdZjQgXkIlNJAEOk1eu7q0l1nE,13475
+xmipp3/protocols/protocol_reconstruct_highres.py,sha256=vcIvqWmfhTNE7X6HnPlPrCD2choZN88n1pHWOJhw8Z0,108240
 xmipp3/protocols/protocol_reconstruct_significant.py,sha256=VMHCDpc-XKe43jjyPuswFRdu9l3s-eXyUxIUjfvi4bc,26462
 xmipp3/protocols/protocol_reconstruct_swarm.py,sha256=z_g7HJ6Ix_Ov3zCzLnqkJuPb3vKq82UYCpB87Cles_E,30163
 xmipp3/protocols/protocol_resolution3d.py,sha256=L9e46RaZosxZlfFOi_GCuwNGqxY13LTxrqrwejWiPFE,10241
@@ -92,20 +96,20 @@ xmipp3/protocols/protocol_screen_deeplearning.py,sha256=nrhfzoTWPWULTrDDnUD1ELCC
 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=iejnfsJkYEJhs9cADX5_r7Iniwnnc8X-nwF4RbU1ADU,5138
-xmipp3/protocols/protocol_simulate_ctf.py,sha256=nVzve11NPeHOidJtxZ3oPKhgoGeMbiK9BSSP81n6fHU,8047
+xmipp3/protocols/protocol_simulate_ctf.py,sha256=r-9FgH5J1RT_Pcokm4LSoJgMYv0vra7HnrhSIDuiIG0,8044
 xmipp3/protocols/protocol_structure_map.py,sha256=Nf6H_imnkgJTs64-I8FFFtD1CKFmaZ8Sb6ZTD_j33m8,8331
 xmipp3/protocols/protocol_structure_map_zernike3d.py,sha256=EY7rV6vSfyxYXH3ed0FTzNsYu87Ph9klYGqlwuc0eyU,22110
-xmipp3/protocols/protocol_subtract_projection.py,sha256=v1svDU_qGWBu58oGrTVSIB8cJj3INE3Dl97E2DoaXuU,12850
-xmipp3/protocols/protocol_tilt_analysis.py,sha256=uw_kNUPw1LuG75mQmXkL9xHPAIc5xTXRRrbHVN0qJF0,28556
-xmipp3/protocols/protocol_trigger_data.py,sha256=8eJiHieg7wHX0Gd7ytyfLHnnyzYMpayVda1v6vFHWvs,15711
-xmipp3/protocols/protocol_validate_fscq.py,sha256=fY54lDWAWcdw2zPlnf5DNV98y0v-qgjkJiKWHqIS3nY,26475
+xmipp3/protocols/protocol_subtract_projection.py,sha256=VnXv2WVH3iqM5rzZIBnM_5hDGVADx0zgFvZakwyMjUI,15023
+xmipp3/protocols/protocol_tilt_analysis.py,sha256=JYeeZoQxPyGpEjjakJQwkTah-0syqIPM9PfQ0gMMQfc,24040
+xmipp3/protocols/protocol_trigger_data.py,sha256=_0eTUdR3X-Wy0D9gs2HFE5YlieMhCnS3_GMLEQB-E8U,16540
+xmipp3/protocols/protocol_validate_fscq.py,sha256=M9UO6OGomuOZAfnalklC0IK_oDhBDR79_nsLrp55bbg,26472
 xmipp3/protocols/protocol_validate_nontilt.py,sha256=0HFI6bnvSzduzBNddaL-WMyM7M4n-K68g3hd1ZC4mc8,16316
 xmipp3/protocols/protocol_validate_overfitting.py,sha256=QYKu8Hi6QwbbEsY5V6Riu7K7PWUpj8oS__ZjobjFe80,25116
-xmipp3/protocols/protocol_volume_adjust_sub.py,sha256=HESmNsxutaxtiO0NO7Wgcj7yncGm_o97bgIB6fkblX8,17626
+xmipp3/protocols/protocol_volume_adjust_sub.py,sha256=vkBPw1dU1P2gwi2dPgLtxSK13ugA97WP9PDCag-fVCA,17477
 xmipp3/protocols/protocol_volume_consensus.py,sha256=miaQo_ldhwAcFefBjIk32iKFpK0SBvaPaVPviD1eoL8,5626
 xmipp3/protocols/protocol_volume_deform_zernike3d.py,sha256=fpZlYE6TRkDkgD4Ozo4RWNCX-ba89bGvqBSn-6Ki8qA,10165
 xmipp3/protocols/protocol_volume_local_adjust.py,sha256=XupsyYS92ClxM34d1PYK8W2X9XNpAoJRREkMWth1CU4,6051
-xmipp3/protocols/protocol_volume_local_sharpening.py,sha256=iFjA4DKEIVKVE1ekNfbCrMWeTRBQwIjXJIQu7DwbP24,12479
+xmipp3/protocols/protocol_volume_local_sharpening.py,sha256=aj2mMfdMz31ACMbKDRhksCzNouro-CZJtQn9JnoHrdM,13402
 xmipp3/protocols/protocol_volume_strain.py,sha256=OQU0mLlHBK0add_gP9hWwDc19FxGAYY4XmjRkKfcB3M,6777
 xmipp3/protocols/protocol_write_testC.py,sha256=LfUhtQeT_lsZjw7yHDa0B-m33V-UmfJYMn_fFyruPnc,3288
 xmipp3/protocols/protocol_write_testP.py,sha256=2CaljDnQFTCIq7Jg6OdQjJmWHOOGpLPgdvyaN2E6cbs,4485
@@ -143,29 +147,29 @@ xmipp3/tests/test_protocol_simulate_ctf.py,sha256=G1PImqwh0ZEOfpl6RK6xeUqJmWIE2J
 xmipp3/tests/test_protocol_validate_fscq.py,sha256=RL8UTe8tgn_IU8mazmuiQzfFQjmoJkZHxi-96rtDInI,2699
 xmipp3/tests/test_protocol_validate_overfitting.py,sha256=PSFRoARteTABLZxJ4ZuWJUnh34QT2JQ6gekqOTgpG6w,3598
 xmipp3/tests/test_protocols_add_noise.py,sha256=Uc6Kc5KaxXUeX6GedbHV3h7svSQoPrXfbHsqc6J6BQk,5209
-xmipp3/tests/test_protocols_angular_resolution_alignment.py,sha256=pVhSBXI4vs025a0LYI8sogFDWPz9uOlC5wuLpqcViBE,3874
 xmipp3/tests/test_protocols_continuousflex.py,sha256=y_WeCm-XiZ5rJS1lx4i0TsGoWNf3TeHwL3RC7vVr_Q4,6940
 xmipp3/tests/test_protocols_deepVolPostprocessing.py,sha256=ZUSkLaR2sRlvZoaWPYwIUmDBC0X5DRy7peRd8EieseY,7143
+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=cDvRxn6JUI1WQhXjT-83u32hOETBDxt-F5F_ZFx0wJI,4411
 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_mixed_movies.py,sha256=kAAqNx33TMoOH0v6TaTyfUvdSAQ-vEtUalf6ecgepsM,6151
 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=wJJqrX3ALeeZ8xFNcCO7ThE2dJG4p3yM6ua-7m76UJg,82720
-xmipp3/tests/test_protocols_xmipp_3d.py,sha256=xj1AMmrKmSjyqj6Q8HOD3jWBypYQ48bXYtxca8f1QGw,171944
-xmipp3/tests/test_protocols_xmipp_mics.py,sha256=yXjq85Y4xrxKGT9LO5N4fXb4gbGYGDPBRrJKiDlLIRI,59915
+xmipp3/tests/test_protocols_xmipp_2d.py,sha256=MVN0CQQil2cIxX4ju5rsk0Qv8grsZ-_Sln9ugPKvWTo,83556
+xmipp3/tests/test_protocols_xmipp_3d.py,sha256=88LUfNyl1OxYdPF9tocn3K_vm3NQ9_9R1grbQhiSMq4,113442
+xmipp3/tests/test_protocols_xmipp_mics.py,sha256=Bf-heIcImLR74DcYvS5_6xrwVu84OwQ_TYP3feenDAQ,61478
 xmipp3/tests/test_protocols_xmipp_movie_resize.py,sha256=XR1gYYZeDhNOkDkZhimPDbqcYwss5z-zbhJ73ZM0a5g,6494
-xmipp3/tests/test_protocols_xmipp_movies.py,sha256=iINRMOxegyXVjLrAx-KtkWtxArxRcpuK-9E_UYSBqcY,42089
+xmipp3/tests/test_protocols_xmipp_movies.py,sha256=Nl8zfskXUTgfag7I0zrJ3iP44YMv9jiUX0cp5lTBuy4,34504
 xmipp3/tests/test_protocols_zernike3d.py,sha256=bTXCK4wBKSJZK1KCZXec3j8y1mVLoBxE5bF3AGbOsNs,18132
-xmipp3/viewers/__init__.py,sha256=q1G63LhmRxGiPwCa35-gatZXKSbftApQFvBXaL1vLjc,3542
+xmipp3/viewers/__init__.py,sha256=UHKwvYfhP4_FeyOPihwvGEbKcrorMOHS8AXeW3Yl6KQ,3669
 xmipp3/viewers/plotter.py,sha256=YHDqAs7_rbv8cXMmwmg42YeeBnesdX44awrppX3VJw0,3875
 xmipp3/viewers/viewer.py,sha256=X68yRXVraMmzmoHaccntfuZBVXvnx49hfCsXyBLmlH4,19233
 xmipp3/viewers/viewer_analyze_local_ctf.py,sha256=-Oa7flu05KxP8M6AlZRaWKCRqZljRz23Z6Ncz1qDHhw,4866
-xmipp3/viewers/viewer_angular_resolution_alignment.py,sha256=9DCZ94TAedHltvlKf99BEFtgFuoMisKipMwubPn82lU,5155
+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_ctf_consensus.py,sha256=gosd9D2iuTUHgdlQlHIGS_HBybThR1S8SBfgM096e_8,7669
 xmipp3/viewers/viewer_deepEMHancer.py,sha256=ok5e2NfPeK8Joa0Y7Wp0GQG00Pk7AAG19xOE42A1l6c,5741
@@ -176,7 +180,7 @@ xmipp3/viewers/viewer_eliminate_empty_images.py,sha256=LMDYe4iql1kFOESBbwyClzNez
 xmipp3/viewers/viewer_extract_asymmetric_unit.py,sha256=fGYqUfrsPLzFDj4UxuVQe8b2AN_I64cruaWBjhnLkU8,7092
 xmipp3/viewers/viewer_local_sharpening.py,sha256=_j_4RZISQjWzrBFmsI88DrNqxbT3Ng1AJRmo0MfdCCk,4408
 xmipp3/viewers/viewer_ml2d.py,sha256=XL1NL8mg-W8TC0fHemD-eR9mHxgUMBnF2d9gwJagC7s,8451
-xmipp3/viewers/viewer_movie_alignment.py,sha256=mOrF2xxy3eA2q_xVnH46We4ECrhC9y5xR62Sk6rwG_c,7122
+xmipp3/viewers/viewer_movie_alignment.py,sha256=h2mDRK_hBNN97E5nqvVkTYtgCl8b7MNz181uZMb97qs,6763
 xmipp3/viewers/viewer_normalize_strain.py,sha256=L54CZvxaU9ezu223jgvOSTBn4yYWs2x9q87_3vvHi9k,2804
 xmipp3/viewers/viewer_pdb_deform_zernike3d.py,sha256=g5-ntcOt7841rFFGPRb6NK-wQ2FfbBz2P1E980uENZo,4653
 xmipp3/viewers/viewer_projmatch.py,sha256=j9_1S8hrTUjRL-YeIYdLvxvsTTBjrJR9TyRQN3gG3JY,37619
@@ -198,9 +202,9 @@ 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-24.6.0.0.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-scipion_em_xmipp-24.6.0.0.dist-info/METADATA,sha256=e5mEXzj7v4bn5xf7M_k_edNq3EJtZMamwdbq220Yt4E,1621
-scipion_em_xmipp-24.6.0.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-scipion_em_xmipp-24.6.0.0.dist-info/entry_points.txt,sha256=uAfbaIdLcZ7JWL0tWzQVwsVEyyOZb1WcBX4YZMqRrIk,37
-scipion_em_xmipp-24.6.0.0.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
-scipion_em_xmipp-24.6.0.0.dist-info/RECORD,,
+scipion_em_xmipp-24.12.2.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+scipion_em_xmipp-24.12.2.dist-info/METADATA,sha256=Wc7YocK5Bm0u0NNYEU7dMWzX72VqY8h54Nl8BZQMYfQ,1636
+scipion_em_xmipp-24.12.2.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+scipion_em_xmipp-24.12.2.dist-info/entry_points.txt,sha256=uAfbaIdLcZ7JWL0tWzQVwsVEyyOZb1WcBX4YZMqRrIk,37
+scipion_em_xmipp-24.12.2.dist-info/top_level.txt,sha256=qnLFoZzwKticb33xgeSAJv3P7nD2nHMTFKYzxAorOOQ,7
+scipion_em_xmipp-24.12.2.dist-info/RECORD,,

{scipion_em_xmipp-24.6.0.0.dist-info → scipion_em_xmipp-24.12.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: bdist_wheel (0.45.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

xmipp3/__init__.py

@@ -27,36 +27,59 @@
 # **************************************************************************
 
 import json
-import subprocess
 from datetime import datetime
-
-from pyworkflow import Config
 import pwem
+from pyworkflow import Config
 import pyworkflow.utils as pwutils
-
+from scipion.install.funcs import CommandDef
+from scipion import __version__ as scipionAppVersion
+from packaging.version import Version
 from .base import *
-from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME
+from .version import *
+from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME, XMIPP_CUDA_BIN, XMIPP_CUDA_LIB, XMIPP_GIT_URL
 
-type_of_version = 'release' #'devel'
-_logo = "xmipp_logo" + ("" if type_of_version == 'release' else '_devel') + '.png'
 
 _references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
-_currentBinVersion = '3.24.06.0'
-__version__ = _currentBinVersion[2:] + ".0"  # Set this to ".0" on each xmipp binary release, otherwise increase it --> ".1", ".2", ...
-
+_currentDepVersion = '1.0'
 # Requirement version variables
 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__
+
+
 class Plugin(pwem.Plugin):
     _homeVar = XMIPP_HOME
     _pathVars = [XMIPP_HOME]
     _supportedVersions = []
     _url = XMIPP_URL
     _condaRootPath = None
-
+    # Refressing the plugin
+    # Inspects the call stack to find 'installPipModule' and sets 'self._plugin' to None.
+    # Uses CPython's internal API 'PyFrame_LocalsToFast' to sync changes.
+    # Risky and CPython-specific; use only if redesign is not possible.
+    try:
+        import inspect
+        import ctypes
+        for frameInfo in inspect.stack():
+            if frameInfo.function == "installPipModule":
+                frame = frameInfo[0]
+                frame.f_locals['self']._plugin = None
+                ctypes.pythonapi.PyFrame_LocalsToFast(
+				    ctypes.py_object(frame),
+				    ctypes.c_int(1))
+    except Exception as e:
+        print(e)
+    
     @classmethod
     def _defineVariables(cls):
-        cls._addVar(XMIPP_HOME, pwem.Config.XMIPP_HOME)
+        cls._defineEmVar(XMIPP_HOME, pwem.Config.XMIPP_HOME)
+        cls._defineVar(XMIPP_CUDA_BIN, pwem.Config.CUDA_BIN)
+        cls._defineVar(XMIPP_CUDA_LIB, pwem.Config.CUDA_LIB)
 
     @classmethod
     def getEnviron(cls, xmippFirst=True):
@@ -65,8 +88,8 @@ class Plugin(pwem.Plugin):
         pos = pwutils.Environ.BEGIN if xmippFirst else pwutils.Environ.END
 
         environ.update({
-            'PATH': pwem.Config.CUDA_BIN,
-            'LD_LIBRARY_PATH': pwem.Config.CUDA_LIB
+            'PATH': cls.getVar(XMIPP_CUDA_BIN),
+            'LD_LIBRARY_PATH': cls.getVar(XMIPP_CUDA_LIB)
         }, position=pwutils.Environ.END)
 
         if os.path.isfile(getXmippPath('xmippEnv.json')):
@@ -117,94 +140,88 @@ class Plugin(pwem.Plugin):
             Scipion-defined software can be used as dependencies
             by using its name as string.
         """
+        
+        # Determine if we are on a development 
+        bundleDir = cls.__getBundleDirectory()
+        develMode = bundleDir is not None
+        
+        COMPILE_TARGETS = [
+            'dist/bin/xmipp_image_header', 
+            'dist/xmipp.bashrc'
+        ]
+        
+        # When changing dependencies, increment _currentDepVersion
+        CONDA_DEPENDENCIES = [
+            'cmake>=3.17',
+            'hdf5>=1.18',
+            'sqlite>=3',
+            'fftw>=3',
+            'mpich-mpicxx',
+            'c-compiler',
+            'cxx-compiler',
+            'make',
+            'openjdk',
+            'libtiff',
+            'libjpeg-turbo'
+        ]
+        
+        if os.environ['CONDA_PREFIX'] is not None: # TODO replace with pyworkflow method when available.
+            commands = CommandDef('conda install -c conda-forge '  + ' '.join(CONDA_DEPENDENCIES))
+            env.addPackage(
+                'xmippDep', version=_currentDepVersion,
+                tar='void.tgz',
+                commands=commands.getCommands(),
+                neededProgs=['conda'],
+                default=False
+            )
+        
+        if develMode:
+            env.addPackage(
+                'xmippDev',
+                tar='void.tgz',
+                commands=[(f'cd {bundleDir} && ./xmipp', COMPILE_TARGETS)],
+                neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
+                updateCuda=True,
+                default=False
+            )
+        
+        xmippSrc = f'xmippSrc-{version._binTagVersion}'
+        installCommands = [
+            (f'cd .. && rm -rf {xmippSrc} && '
+            f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
+            f'cd {xmippSrc} && '
+            f'git checkout {version._binTagVersion} && '
+            f'./xmipp --production True ', COMPILE_TARGETS)
+        ]
+        env.addPackage(
+            'xmippSrc', version=version._binTagVersion,
+            tar='void.tgz',
+            commands=installCommands,
+            neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
+            updateCuda=True,
+            default=not develMode
+        )
+        
+        ## EXTRA PACKAGES ##
+        installDeepLearningToolkit(cls, env)
 
-        ## XMIPP SOFTWARE ##
-        xmippDeps = []  # Deps should be at requirements.txt (old: scons, joblib, scikit_learn)
-
-        # Installation vars for commands formating
-        verToken = getXmippPath('v%s' % _currentBinVersion)
-        confToken = getXmippPath("xmipp.conf")
-        installVars = {'installedToken': "installation_finished",
-                       'bindingsToken': "bindings_linked",
-                       'verToken': verToken,
-                       'nProcessors': env.getProcessors(),
-                       'xmippHome': getXmippPath(),
-                       'bindingsSrc': getXmippPath('bindings', 'python'),
-                       'bindingsDst': Config.getBindingsFolder(),
-                       'xmippLib': getXmippPath('lib', 'libXmipp.so'),
-                       'coreLib': getXmippPath('lib', 'libXmippCore.so'),
-                       'libsDst': Config.getLibFolder(),
-                       'confToken': confToken,
-                       'strPlaceHolder': '%s',  # to be replaced in the future
-                       'currVersion': _currentBinVersion
-                       }
-
-        ## Installation commands (removing bindingsToken)
-        installCmd = ("cd {cwd} && {configCmd} && {compileCmd} N={nProcessors:d} && "
-                      "ln -srfn build {xmippHome} && cd - && "
-                      "touch {installedToken} && rm {bindingsToken} 2> /dev/null")
-        installTgt = [getXmippPath('bin', 'xmipp_reconstruct_significant'),
-                      getXmippPath("lib/libXmippJNI.so"),
-                      installVars['installedToken']]
-
-        ## Linking bindings (removing installationToken)
-        bindingsAndLibsCmd = ("find {bindingsSrc} -maxdepth 1 -mindepth 1 "
-                              r"! -name __pycache__ -exec ln -srfn {{}} {bindingsDst} \; && "
-                              "ln -srfn {coreLib} {libsDst} && "
-                              "touch {bindingsToken} && "
-                              "rm {installedToken} 2> /dev/null")
-        bindingsAndLibsTgt = [os.path.join(Config.getBindingsFolder(), 'xmipp_base.py'),
-                              os.path.join(Config.getBindingsFolder(), 'xmippLib.so'),
-                              os.path.join(Config.getLibFolder(), 'libXmipp.so'),
-                              installVars['bindingsToken']]
-
-        sourceTgt = [getXmippPath('xmipp.bashrc')]  # Target for xmippSrc and xmippDev
-        ## Allowing xmippDev if devel mode detected
+    @classmethod
+    def __getBundleDirectory(cls):
         # plugin  = scipion-em-xmipp  <--  xmipp3    <--     __init__.py
         pluginDir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
         # bundle  = xmipp-bundle  <-  src   <-  scipion-em-xmipp
         bundleDir = os.path.dirname(os.path.dirname(pluginDir))
 
-        isPypiDev = os.path.isfile(os.path.join(pluginDir, 'setup.py'))
-        isXmippBu = (os.path.isdir(os.path.join(bundleDir, 'src')) and
-                     os.path.isfile(os.path.join(bundleDir, 'xmipp')))
-        develMode = isPypiDev and isXmippBu
-        if develMode:
-            env.addPackage('xmippDev', tar='void.tgz',
-                           commands=[(installCmd.format(**installVars,
-                                                        cwd=bundleDir,
-                                                        configCmd='pwd',
-                                                        compileCmd='./xmipp all'),
-                                      installTgt+sourceTgt),
-                                     (bindingsAndLibsCmd.format(**installVars),
-                                      bindingsAndLibsTgt)],
-                           deps=xmippDeps, default=False)
-
-        avoidConfig = os.environ.get('XMIPP_NOCONFIG', 'False') == 'True'
-        alreadyCompiled = os.path.isfile(getXmippPath('v' + _currentBinVersion))  # compilation token (see the xmipp script)
-        configSrc = ('./xmipp check_config' if avoidConfig
-                     else './xmipp config noAsk && ./xmipp check_config')
-        env.addPackage('xmippSrc', version=_currentBinVersion,
-                       # adding 'v' before version to fix a package target (post-link)
-                       tar='xmippSrc-v' + _currentBinVersion + '.tgz',
-                       commands=[(installCmd.format(**installVars, cwd='.',
-                                                    configCmd=configSrc,
-                                                    compileCmd='./xmipp compileAndInstall'),
-                                  installTgt + sourceTgt),
-                                 (bindingsAndLibsCmd.format(**installVars),
-                                  bindingsAndLibsTgt)],
-                       deps=xmippDeps, default=not (develMode or alreadyCompiled))
-
-        ## EXTRA PACKAGES ##
-        installDeepLearningToolkit(cls, env)
-
-
+        isBundle = (os.path.isdir(os.path.join(bundleDir, 'src')) and
+                    os.path.isfile(os.path.join(bundleDir, 'xmipp')))
+        
+        return bundleDir if isBundle else None
+    
 def installDeepLearningToolkit(plugin, env):
 
     preMsgs = []
     cudaMsgs = []
     nvidiaDriverVer = None
-    useGpu = False
     if os.environ.get('CUDA', 'True') == 'True':
         try:
             nvidiaDriverVer = subprocess.Popen(["nvidia-smi",
@@ -221,7 +238,7 @@ def installDeepLearningToolkit(plugin, env):
                                 f"To enable CUDA (drivers>{NVIDIA_DRIVERS_MINIMUM_VERSION} needed), "
                                 "set CUDA=True in 'scipion.conf' file")
                 nvidiaDriverVer = None
-        except (ValueError, TypeError):
+        except (ValueError, TypeError, FileNotFoundError):
             nvidiaDriverVer = None
             preMsgs.append("Not nvidia driver found. Type: "
                            " nvidia-smi --query-gpu=driver_version --format=csv,noheader")
@@ -230,6 +247,7 @@ def installDeepLearningToolkit(plugin, env):
             msg = ("Tensorflow installed without GPU. Just CPU computations "
                    "enabled (slow computations).")
             cudaMsgs.append(msg)
+            useGpu = False
 
     if nvidiaDriverVer is not None:
         preMsgs.append("CUDA support found. Driver version: %s" % nvidiaDriverVer)

xmipp3/checkProtocolsConf.py

@@ -0,0 +1,117 @@
+# ***************************************************************************
+# * Authors:		 Carlos Oscar Sorzano (coss@cnb.csic.es)
+# *
+# *
+# * 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'
+# ***************************************************************************/
+'''
+Description: This script checks for any protocols missing in the file 
+             protocols.conf and lists them for further action.
+
+Usage: python check_missing_protocols.py
+'''
+
+import ast
+import glob
+import os
+
+def get_classes_from_file(file_path):
+    with open(file_path, 'r', encoding='utf-8') as file:
+        file_content = file.read()
+        tree = ast.parse(file_content)
+        class_names = [node.name for node in ast.walk(tree) if isinstance(node, ast.ClassDef)]
+        return class_names
+
+with open("protocols.conf", 'r', encoding='utf-8') as file:
+    protocolsConf = file.read()
+
+blackList = ['ScatterImageMarker','XMIPPCOLUMNS', 'XmippProtVolAdjBase', 'AlignVolPartOutputs','ProtPickingConsensusOutput',
+             'XmippProtEliminateEmptyBase', 'XmippProtDeepConsSubSet', 'XmippProtWriteTestP', 'NoOutputGenerated','XmippProtSubtractProjectionBase',
+             'XmippProtWriteTestC','KendersomBaseClassify','XmippProtAlignVolumeForWeb', 'XMIPPCOLUMNS', 'NoOutputGenerated', 'ScatterImageMarker',
+             'AlignVolPartOutputs']
+
+
+#######Missing classes
+missingCounter = 0
+classCounter = 0
+for py_file in glob.glob("protocols/*.py"):
+    for class_name in get_classes_from_file(py_file):
+        classCounter+=1
+        if not class_name in blackList:
+            if not class_name in protocolsConf:
+                print(f"Missing: {class_name} from {py_file}")
+                missingCounter +=1
+print(f"Missing classes: {missingCounter}/{classCounter}")
+
+
+
+#######Missing tests
+
+def extract_protocols_from_file(file_path):
+	"""Extrae las llamadas a self.newProtocol en un archivo."""
+	protocols = []
+	with open(file_path, 'r', encoding='utf-8') as f:
+		source_code = f.read()
+	tree = ast.parse(source_code)
+	for node in ast.walk(tree):
+		if isinstance(node, ast.Call):
+			if (isinstance(node.func, ast.Attribute) and
+					node.func.attr == "newProtocol" and
+					isinstance(node.func.value, ast.Name) and
+					node.func.value.id == "self"):
+				if node.args:
+					protocol_node = node.args[0]
+					if isinstance(protocol_node, ast.Name):
+						protocol = protocol_node.id
+					elif isinstance(protocol_node, ast.Attribute):
+						protocol = protocol_node.attr
+					elif isinstance(protocol_node, ast.Constant):
+						protocol = protocol_node.value
+					if protocol not in protocols:
+						protocols.append(protocol)
+	return protocols
+
+
+def extract_protocols_from_folder(folder_path):
+	"""Extrae todos los protocolos de los archivos .py en una carpeta."""
+	protocolsFull= []
+	for root, _, files in os.walk(folder_path):
+		for file in files:
+			if file.endswith(".py"):
+				file_path = os.path.join(root, file)
+				protocols = extract_protocols_from_file(file_path)
+				for protocol in protocols:
+					if protocol not in protocolsFull:
+						protocolsFull.append(protocol)
+	return protocolsFull
+
+folder_path = "tests/"
+protocols = extract_protocols_from_folder(folder_path)
+partProt = protocols.index('xpsp')
+protocols[partProt] = 'XmippProtScreenParticles'
+
+protocolsWithoutTest = []
+for py_file in glob.glob("protocols/*.py"):
+    for class_name in get_classes_from_file(py_file):
+	    if not class_name in blackList:
+		    if class_name not in protocols:
+			    protocolsWithoutTest.append(class_name)
+		    
+print(f"\nProtocolos without test ({len(protocolsWithoutTest)}/{len(protocols)})")
+print('\n'.join(protocolsWithoutTest))

xmipp3/constants.py

@@ -28,10 +28,13 @@ This modules contains constants related to Xmipp3 protocols
 """
 
 # ------------------ Constants values --------------------------------------
+XMIPP_GIT_URL = 'https://github.com/I2PC/xmipp.git'
 XMIPP_URL = 'https://github.com/i2pc/scipion-em-xmipp'
 XMIPP_HOME = 'XMIPP_HOME'
 NMA_HOME = 'NMA_HOME'
 XMIPP_DLTK_NAME = 'deepLearningToolkit'  # consider to change it to xmipp_DLTK to make short it
+XMIPP_CUDA_BIN = 'XMIPP_CUDA_BIN'
+XMIPP_CUDA_LIB = 'XMIPP_CUDA_LIB'
 
 MASK_FILL_VALUE = 0
 MASK_FILL_MIN = 1