From 9e082233222f7c4061477679f08ad28b5d06d142 Mon Sep 17 00:00:00 2001 From: Matteo Visconti dOC Date: Wed, 25 May 2016 16:51:58 -0400 Subject: [PATCH 1/3] DOC: update readme to reflect current output --- README.md | 87 ++++++++++++++++++++++++++++++------------------------- 1 file changed, 48 insertions(+), 39 deletions(-) diff --git a/README.md b/README.md index 2cc8c9c..57ba940 100644 --- a/README.md +++ b/README.md @@ -96,66 +96,75 @@ in current directory: $> python -m duecredit examples/example_scipy.py I: Simulating 4 blobs I: Done clustering 4 blobs + DueCredit Report: - - scipy (v 0.14.1) [1] - - scipy.cluster.hierarchy:linkage (Single linkage hierarchical clustering) [2] - - numpy (v 1.8.2) [3] - - 2 modules cited - 1 functions cited - + - Scientific tools library / scipy (v 0.14) [1] + - Single linkage hierarchical clustering / scipy.cluster.hierarchy:linkage (v 0.14) [2] + + 1 package cited + 0 modules cited + 1 function cited + References ---------- - + [1] Jones, E. et al., 2001. SciPy: Open source scientific tools for Python. - [2] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link - cluster method. The Computer Journal, 16(1), pp.30–34. - [3] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The - NumPy array: a structure for efficient numerical - computation. Computing in Science & Engineering, 13(2), pp.22–30. + [2] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. Incremental runs of various software would keep enriching that file. Then you can use `duecredit summary` command to show that information again (stored in `.duecredit.p` file) or export it as a BibTeX file ready for reuse, e.g.: - $> venv/bin/duecredit summary --format=bibtex - @book{sokal1958statistical, - author = {Sokal, R R and Michener, C D and {University of Kansas}}, - title = {{A Statistical Method for Evaluating Systematic Relationships}}, - publisher = {University of Kansas}, - year = {1958}, - series = {University of Kansas science bulletin} + $> duecredit summary --format=bibtex + @Misc{JOP+01, + author = {Eric Jones and Travis Oliphant and Pearu Peterson and others}, + title = {{SciPy}: Open source scientific tools for {Python}}, + year = {2001--}, + url = "http://www.scipy.org/", + note = {[Online; accessed 2015-07-13]} } - @book{jain1988algorithms, - title={Algorithms for clustering data}, - author={Jain, Anil K and Dubes, Richard C}, - year={1988}, - publisher={Prentice-Hall, Inc.} + @article{sibson1973slink, + title={SLINK: an optimally efficient algorithm for the single-link cluster method}, + author={Sibson, Robin}, + journal={The Computer Journal}, + volume={16}, + number={1}, + pages={30--34}, + year={1973}, + publisher={Br Computer Soc} } - ... - and if by default only references for "implementation" are listed, we can enable listing of references for other tags as well (e.g. "edu" depicting instructional materials -- textbooks etc on the topic): $> DUECREDIT_REPORT_TAGS=* duecredit summary + DueCredit Report: - - scipy (v 0.14.1) [1, 2, 3, 4, 5, 6, 7, 8] - - scipy.cluster.hierarchy:linkage (Single linkage hierarchical clustering) [9] - - numpy (v 1.8.2) [10] - - 2 modules cited - 1 functions cited - + - Scientific tools library / numpy (v 1.9.2) [1] + - Scientific tools library / scipy (v 0.14) [2] + - Hierarchical clustering / scipy.cluster.hierarchy (v 0.14) [3, 4, 5, 6, 7, 8, 9] + - Single linkage hierarchical clustering / scipy.cluster.hierarchy:linkage (v 0.14) [10] + + 2 packages cited + 1 module cited + 1 function cited + References ---------- - - [1] Sokal, R.R., Michener, C.D. & University of Kansas, 1958. A Statistical Method for Evaluating Systematic Relationships, University of Kansas. - [2] Jain, A.K. & Dubes, R.C., 1988. Algorithms for clustering data, Prentice-Hall, Inc.. - [3] Johnson, S.C., 1967. Hierarchical clustering schemes. Psychometrika, 32(3), pp.241–254. - ... + + [1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. + [2] Jones, E. et al., 2001. SciPy: Open source scientific tools for Python. + [3] Sneath, P.H. & Sokal, R.R., 1962. Numerical taxonomy. Nature, 193(4818), pp.855–860. + [4] Batagelj, V. & Bren, M., 1995. Comparing resemblance measures. Journal of classification, 12(1), pp.73–90. + [5] Sokal, R.R., Michener, C.D. & University of Kansas, 1958. A Statistical Method for Evaluating Systematic Relationships, University of Kansas. + [6] Jain, A.K. & Dubes, R.C., 1988. Algorithms for clustering data, Prentice-Hall, Inc.. + [7] Johnson, S.C., 1967. Hierarchical clustering schemes. Psychometrika, 32(3), pp.241–254. + [8] Edelbrock, C., 1979. Mixture model tests of hierarchical clustering algorithms: + the problem of classifying everybody. Multivariate Behavioral Research, 14(3), pp.367–384. + [9] Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Annals of eugenics, 7(2), pp.179–188. + [10] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. Ultimate goals From 8178e6f294319cd4be7cf614ce3309e21b1ae8b5 Mon Sep 17 00:00:00 2001 From: Matteo Visconti dOC Date: Wed, 25 May 2016 16:53:39 -0400 Subject: [PATCH 2/3] DOC: fix small change to readme --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 57ba940..fb738e0 100644 --- a/README.md +++ b/README.md @@ -161,8 +161,7 @@ depicting instructional materials -- textbooks etc on the topic): [5] Sokal, R.R., Michener, C.D. & University of Kansas, 1958. A Statistical Method for Evaluating Systematic Relationships, University of Kansas. [6] Jain, A.K. & Dubes, R.C., 1988. Algorithms for clustering data, Prentice-Hall, Inc.. [7] Johnson, S.C., 1967. Hierarchical clustering schemes. Psychometrika, 32(3), pp.241–254. - [8] Edelbrock, C., 1979. Mixture model tests of hierarchical clustering algorithms: - the problem of classifying everybody. Multivariate Behavioral Research, 14(3), pp.367–384. + [8] Edelbrock, C., 1979. Mixture model tests of hierarchical clustering algorithms: the problem of classifying everybody. Multivariate Behavioral Research, 14(3), pp.367–384. [9] Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Annals of eugenics, 7(2), pp.179–188. [10] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. From 3d271a04ccff95e80de7acca9a33812230334522 Mon Sep 17 00:00:00 2001 From: Matteo Visconti dOC Date: Thu, 26 May 2016 08:59:02 -0400 Subject: [PATCH 3/3] DOC: Update readme --- README.md | 45 ++++++++++++++++++++++++++++++--------------- 1 file changed, 30 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index fb738e0..39fae00 100644 --- a/README.md +++ b/README.md @@ -96,20 +96,23 @@ in current directory: $> python -m duecredit examples/example_scipy.py I: Simulating 4 blobs I: Done clustering 4 blobs - + DueCredit Report: - - Scientific tools library / scipy (v 0.14) [1] - - Single linkage hierarchical clustering / scipy.cluster.hierarchy:linkage (v 0.14) [2] - - 1 package cited + - Scientific tools library / numpy (v 1.10.4) [1] + - Scientific tools library / scipy (v 0.14) [2] + - Single linkage hierarchical clustering / scipy.cluster.hierarchy:linkage (v 0.14) [3] + + 2 packages cited 0 modules cited 1 function cited - + References ---------- - - [1] Jones, E. et al., 2001. SciPy: Open source scientific tools for Python. - [2] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. + + [1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. + [2] Jones, E. et al., 2001. SciPy: Open source scientific tools for Python. + [3] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. + Incremental runs of various software would keep enriching that file. Then you can use `duecredit summary` command to show that information @@ -117,6 +120,16 @@ again (stored in `.duecredit.p` file) or export it as a BibTeX file ready for reuse, e.g.: $> duecredit summary --format=bibtex + @article{van2011numpy, + title={The NumPy array: a structure for efficient numerical computation}, + author={Van Der Walt, Stefan and Colbert, S Chris and Varoquaux, Gael}, + journal={Computing in Science \& Engineering}, + volume={13}, + number={2}, + pages={22--30}, + year={2011}, + publisher={AIP Publishing} + } @Misc{JOP+01, author = {Eric Jones and Travis Oliphant and Pearu Peterson and others}, title = {{SciPy}: Open source scientific tools for {Python}}, @@ -135,6 +148,7 @@ ready for reuse, e.g.: publisher={Br Computer Soc} } + and if by default only references for "implementation" are listed, we can enable listing of references for other tags as well (e.g. "edu" depicting instructional materials -- textbooks etc on the topic): @@ -142,18 +156,18 @@ depicting instructional materials -- textbooks etc on the topic): $> DUECREDIT_REPORT_TAGS=* duecredit summary DueCredit Report: - - Scientific tools library / numpy (v 1.9.2) [1] + - Scientific tools library / numpy (v 1.10.4) [1] - Scientific tools library / scipy (v 0.14) [2] - Hierarchical clustering / scipy.cluster.hierarchy (v 0.14) [3, 4, 5, 6, 7, 8, 9] - - Single linkage hierarchical clustering / scipy.cluster.hierarchy:linkage (v 0.14) [10] - + - Single linkage hierarchical clustering / scipy.cluster.hierarchy:linkage (v 0.14) [10, 11] + 2 packages cited 1 module cited 1 function cited - + References ---------- - + [1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. [2] Jones, E. et al., 2001. SciPy: Open source scientific tools for Python. [3] Sneath, P.H. & Sokal, R.R., 1962. Numerical taxonomy. Nature, 193(4818), pp.855–860. @@ -163,7 +177,8 @@ depicting instructional materials -- textbooks etc on the topic): [7] Johnson, S.C., 1967. Hierarchical clustering schemes. Psychometrika, 32(3), pp.241–254. [8] Edelbrock, C., 1979. Mixture model tests of hierarchical clustering algorithms: the problem of classifying everybody. Multivariate Behavioral Research, 14(3), pp.367–384. [9] Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Annals of eugenics, 7(2), pp.179–188. - [10] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. + [10] Gower, J.C. & Ross, G., 1969. Minimum spanning trees and single linkage cluster analysis. Applied statistics, pp.54–64. + [11] Sibson, R., 1973. SLINK: an optimally efficient algorithm for the single-link cluster method. The Computer Journal, 16(1), pp.30–34. Ultimate goals