From 02e03b06c26bcb34feda035d1a688d62819a0350 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Mon, 30 Jun 2025 20:38:51 +0800 Subject: [PATCH 01/11] add frame and scan id data names to pd_diffractogram --- cif_pow.dic | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/cif_pow.dic b/cif_pow.dic index b7a2f92..9adbe27 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -6291,6 +6291,27 @@ save_PD_DIFFRACTOGRAM save_ +save_pd_diffractogram.diffrn_frame_data_id + + _definition.id '_pd_diffractogram.diffrn_frame_data_id' + _definition.update 2023-10-16 + _description.text +; + A code which identifies the imgCIF frame which was processed to form this + diffractogram. + + See also _pd_diffractogram.diffrn_scan_id. +; + _name.category_id pd_diffractogram + _name.object_id diffrn_frame_data_id + _name.linked_item_id '_diffrn_frame_data.id' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Word + +save_ + save_pd_diffractogram.diffrn_id _definition.id '_pd_diffractogram.diffrn_id' @@ -6310,6 +6331,27 @@ save_pd_diffractogram.diffrn_id save_ +save_pd_diffractogram.diffrn_scan_id + + _definition.id '_pd_diffractogram.diffrn_scan_id' + _definition.update 2025-06-30 + _description.text +; + A code which identifies the imgCIF scan which was processed to form this + diffractogram. + + See also _pd_diffractogram.diffrn_frame_data_id. +; + _name.category_id pd_diffractogram + _name.object_id diffrn_scan_id + _name.linked_item_id '_diffrn_scan.id' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Word + +save_ + save_pd_diffractogram.id _definition.id '_pd_diffractogram.id' From 7f8cbdfcbc901d4833ad06dd14453c4a55acb8db Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 1 Jul 2025 21:29:58 +0800 Subject: [PATCH 02/11] dates --- cif_pow.dic | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index 9adbe27..31ee0ea 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -14,7 +14,7 @@ data_CIF_POW _dictionary.title CIF_POW _dictionary.class Instance _dictionary.version 2.5.0 - _dictionary.date 2025-06-23 + _dictionary.date 2025-07-01 _dictionary.uri https://raw.githubusercontent.com/COMCIFS/Powder_Dictionary/master/cif_pow.dic _dictionary.ddl_conformance 4.2.0 @@ -6294,7 +6294,7 @@ save_ save_pd_diffractogram.diffrn_frame_data_id _definition.id '_pd_diffractogram.diffrn_frame_data_id' - _definition.update 2023-10-16 + _definition.update 2025-07-01 _description.text ; A code which identifies the imgCIF frame which was processed to form this @@ -6334,7 +6334,7 @@ save_ save_pd_diffractogram.diffrn_scan_id _definition.id '_pd_diffractogram.diffrn_scan_id' - _definition.update 2025-06-30 + _definition.update 2025-07-01 _description.text ; A code which identifies the imgCIF scan which was processed to form this @@ -13552,4 +13552,6 @@ save_ information about the wavelength. Added _pd_meas_overall.step_count_time. + + Update PD_DIFFRACTOGRAM to accomodate links to imgCIF scans and frames. ; From 96884000f8352faaf830bba6806f9ff96aaa4e18 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 1 Jul 2025 21:32:25 +0800 Subject: [PATCH 03/11] import img_cif --- cif_pow.dic | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cif_pow.dic b/cif_pow.dic index 31ee0ea..b2dbd61 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -43,6 +43,10 @@ save_PD_GROUP _import.get [ + { + 'dupl':Ignore 'file':cif_img.dic 'mode':Full + 'save':HEAD + }, { 'dupl':Ignore 'file':multi_block_core.dic 'mode':Full 'save':MULTIBLOCK_CORE From 606cc0ad04c701190656f7df2048beb8b0f530f8 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 1 Jul 2025 21:45:40 +0800 Subject: [PATCH 04/11] whitespace --- cif_pow.dic | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cif_pow.dic b/cif_pow.dic index b2dbd61..2e4f36f 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -46,7 +46,7 @@ save_PD_GROUP { 'dupl':Ignore 'file':cif_img.dic 'mode':Full 'save':HEAD - }, + } { 'dupl':Ignore 'file':multi_block_core.dic 'mode':Full 'save':MULTIBLOCK_CORE From 886de6f92c5712b203ef60f3ddb2264c1158bb5e Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 1 Jul 2025 21:54:21 +0800 Subject: [PATCH 05/11] layout & ddlm --- cif_pow.dic | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index 2e4f36f..ffe8fa7 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -44,9 +44,10 @@ save_PD_GROUP _import.get [ { - 'dupl':Ignore 'file':cif_img.dic 'mode':Full - 'save':HEAD - } + 'dupl':Ignore +'file':https://raw.githubusercontent.com/COMCIFS/imgCIF/refs/heads/master/cif_img.dic + 'mode':Full 'save':HEAD + } { 'dupl':Ignore 'file':multi_block_core.dic 'mode':Full 'save':MULTIBLOCK_CORE @@ -13370,7 +13371,7 @@ save_ Deprecated _pd_refln.wavelength_id after consultation with PDDMG. ; - 2.5.0 2025-06-23 + 2.5.0 2025-07-01 ; ## Retain above version number and increment date until final ## release From b251b7281f5fbe7c85280f659d6ad0bacbd7020a Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 1 Jul 2025 22:14:06 +0800 Subject: [PATCH 06/11] adding Checkout the imgCIF dictionary to ddlm workflow --- .github/workflows/main.yml | 20 +++++++++++++------- cif_pow.dic | 4 +--- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 713e72d..a39c93a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -14,7 +14,7 @@ on: branches: [ master ] paths-ignore: - '.github/**' - workflow_dispatch: + workflow_dispatch: # A workflow run is made up of one or more jobs that can run sequentially or in parallel jobs: @@ -27,7 +27,7 @@ jobs: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - name: checkout uses: actions/checkout@v4 - + # Check syntax of all CIF files - name: check_syntax uses: COMCIFS/cif_syntax_check_action@master @@ -43,7 +43,7 @@ jobs: with: path: ~/.julia key: ${{ runner.os }}-julia-v2 - + - name: Install Julia uses: julia-actions/setup-julia@v1 with: @@ -77,13 +77,13 @@ jobs: run: | julia -e 'using Pkg; Pkg.status()' for file in main/*.dic - do + do echo "Checking $file" julia -O0 ./julia_cif_tools/linter.jl -i $PWD/cif_core $file cif_core/ddl.dic - if [ $? != 0 ] - then + if [ $? != 0 ] + then exit 1 ; - fi + fi done ddlm: runs-on: ubuntu-latest @@ -98,6 +98,12 @@ jobs: repository: COMCIFS/cif_core path: cif-dictionaries/cif_core + - name: Checkout the imgCIF dictionary + uses: actions/checkout@v4 + with: + repository: COMCIFS/imgCIF + path: cif-dictionaries/imgCIF + - name: Checkout the multiblock coreCIF dictionary uses: actions/checkout@v4 with: diff --git a/cif_pow.dic b/cif_pow.dic index ffe8fa7..3570acc 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -44,9 +44,7 @@ save_PD_GROUP _import.get [ { - 'dupl':Ignore -'file':https://raw.githubusercontent.com/COMCIFS/imgCIF/refs/heads/master/cif_img.dic - 'mode':Full 'save':HEAD + 'dupl':Ignore 'file':cif_img.dic 'mode':Full 'save':HEAD } { 'dupl':Ignore 'file':multi_block_core.dic 'mode':Full From 8e79d9549fa8036c07a64a30bfa144568bb2fd58 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Fri, 4 Jul 2025 19:48:30 +0800 Subject: [PATCH 07/11] remove _pd_diffractogram.diffrn_frame_data_id --- cif_pow.dic | 33 +++++++-------------------------- 1 file changed, 7 insertions(+), 26 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index 3570acc..9d78b4b 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -6294,27 +6294,6 @@ save_PD_DIFFRACTOGRAM save_ -save_pd_diffractogram.diffrn_frame_data_id - - _definition.id '_pd_diffractogram.diffrn_frame_data_id' - _definition.update 2025-07-01 - _description.text -; - A code which identifies the imgCIF frame which was processed to form this - diffractogram. - - See also _pd_diffractogram.diffrn_scan_id. -; - _name.category_id pd_diffractogram - _name.object_id diffrn_frame_data_id - _name.linked_item_id '_diffrn_frame_data.id' - _type.purpose Link - _type.source Assigned - _type.container Single - _type.contents Word - -save_ - save_pd_diffractogram.diffrn_id _definition.id '_pd_diffractogram.diffrn_id' @@ -6334,19 +6313,20 @@ save_pd_diffractogram.diffrn_id save_ -save_pd_diffractogram.diffrn_scan_id +save_pd_diffractogram.scan_id - _definition.id '_pd_diffractogram.diffrn_scan_id' + _definition.id '_pd_diffractogram.scan_id' _definition.update 2025-07-01 _description.text ; A code which identifies the imgCIF scan which was processed to form this diffractogram. - See also _pd_diffractogram.diffrn_frame_data_id. + The frames which constitute this scan can be determined from the relevant + imgCIF data. ; _name.category_id pd_diffractogram - _name.object_id diffrn_scan_id + _name.object_id scan_id _name.linked_item_id '_diffrn_scan.id' _type.purpose Link _type.source Assigned @@ -13556,5 +13536,6 @@ save_ Added _pd_meas_overall.step_count_time. - Update PD_DIFFRACTOGRAM to accomodate links to imgCIF scans and frames. + Update PD_DIFFRACTOGRAM to link to the imgCIF scan from which the + diffractogram was created. ; From d902fb0ab537331229c82e162677ecc876b171ea Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Fri, 4 Jul 2025 19:58:06 +0800 Subject: [PATCH 08/11] layout & ddlm --- cif_pow.dic | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index 9d78b4b..917d6c7 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -6313,28 +6313,6 @@ save_pd_diffractogram.diffrn_id save_ -save_pd_diffractogram.scan_id - - _definition.id '_pd_diffractogram.scan_id' - _definition.update 2025-07-01 - _description.text -; - A code which identifies the imgCIF scan which was processed to form this - diffractogram. - - The frames which constitute this scan can be determined from the relevant - imgCIF data. -; - _name.category_id pd_diffractogram - _name.object_id scan_id - _name.linked_item_id '_diffrn_scan.id' - _type.purpose Link - _type.source Assigned - _type.container Single - _type.contents Word - -save_ - save_pd_diffractogram.id _definition.id '_pd_diffractogram.id' @@ -6380,6 +6358,28 @@ save_pd_diffractogram.instr_id save_ +save_pd_diffractogram.scan_id + + _definition.id '_pd_diffractogram.scan_id' + _definition.update 2025-07-01 + _description.text +; + A code which identifies the imgCIF scan which was processed to form this + diffractogram. + + The frames which constitute this scan can be determined from the relevant + imgCIF data. +; + _name.category_id pd_diffractogram + _name.object_id scan_id + _name.linked_item_id '_diffrn_scan.id' + _type.purpose Link + _type.source Assigned + _type.container Single + _type.contents Text + +save_ + save_pd_diffractogram.spec_id _definition.id '_pd_diffractogram.spec_id' From 11b8b11730547d77e718f59b8dfcc07d927beb34 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Fri, 4 Jul 2025 20:14:06 +0800 Subject: [PATCH 09/11] not checking out imgCIF --- .github/workflows/main.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a39c93a..3ce38e6 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -98,12 +98,6 @@ jobs: repository: COMCIFS/cif_core path: cif-dictionaries/cif_core - - name: Checkout the imgCIF dictionary - uses: actions/checkout@v4 - with: - repository: COMCIFS/imgCIF - path: cif-dictionaries/imgCIF - - name: Checkout the multiblock coreCIF dictionary uses: actions/checkout@v4 with: From 610d781ad879b1832337886480385528d7ebe0ab Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Tue, 8 Jul 2025 21:50:16 +0800 Subject: [PATCH 10/11] rephrase description --- cif_pow.dic | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/cif_pow.dic b/cif_pow.dic index 56a8352..588326e 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -6417,11 +6417,9 @@ save_pd_diffractogram.scan_id _definition.update 2025-07-01 _description.text ; - A code which identifies the imgCIF scan which was processed to form this - diffractogram. - - The frames which constitute this scan can be determined from the relevant - imgCIF data. + The identifier for the group of imgCIF images used to produce the + diffractogram. Each group of images is known as a scan, and the images + belonging to each scan are described using imgCIF data names. ; _name.category_id pd_diffractogram _name.object_id scan_id @@ -13704,7 +13702,7 @@ save_ Update PD_DIFFRACTOGRAM to link to the imgCIF scan from which the diffractogram was created. - + Update PD_INSTR and PD_INSTR_DETECTOR descriptions. Added _pd_instr.radiation_id and _pd_instr_detector.instr_id. From 85037162e6f78d007945bb56f8df0571e6add418 Mon Sep 17 00:00:00 2001 From: Matthew Rowles Date: Wed, 9 Jul 2025 11:58:08 +0800 Subject: [PATCH 11/11] whitespace --- cif_pow.dic | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cif_pow.dic b/cif_pow.dic index ccab278..e2d2087 100644 --- a/cif_pow.dic +++ b/cif_pow.dic @@ -14376,7 +14376,7 @@ save_ Update PD_DIFFRACTOGRAM to link to the imgCIF scan from which the diffractogram was created. - + Removed _pd_calib_detected_intensity.id as data item and category key of PD_CALIB_DETECTED_INTENSITY.